chr5-177294771-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_022455.5(NSD1):c.7403G>A(p.Arg2468Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2468W) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

NSD1
NM_022455.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.940

Publications

1 publications found

Variant links:

Genes affected

NSD1 (HGNC:14234): (nuclear receptor binding SET domain protein 1) This gene encodes a protein containing a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The encoded protein enhances androgen receptor (AR) transactivation, and this enhancement can be increased further in the presence of other androgen receptor associated coregulators. This protein may act as a nucleus-localized, basic transcriptional factor and also as a bifunctional transcriptional regulator. Mutations of this gene have been associated with Sotos syndrome and Weaver syndrome. One version of childhood acute myeloid leukemia is the result of a cryptic translocation with the breakpoints occurring within nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1 on chromosome 5 and nucleoporin, 98-kd on chromosome 11. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Sep 2018]

NSD1 Gene-Disease associations (from GenCC):

Beckwith-Wiedemann syndrome due to NSD1 mutation
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
Sotos syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen
Sotos syndrome 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics

NSD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.030827075).

BP6

Variant 5-177294771-G-A is Benign according to our data. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294771-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 159439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSD1	NM_022455.5 link	c.7403G>A	p.Arg2468Gln	missense_variant	Exon 23 of 23	ENST00000439151.7	NP_071900.2	Q96L73-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSD1	ENST00000439151.7 link	c.7403G>A	p.Arg2468Gln	missense_variant	Exon 23 of 23	1	NM_022455.5	ENSP00000395929.2		Q96L73-1

Frequencies

GnomAD3 genomes

AF:

0.0000460

AC:

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000478

AC:

AN:

250814

AF XY:

0.0000590

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000176

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000185

AC:

AN:

1461504

Hom.:

Cov.:

AF XY:

0.0000248

AC XY:

AN XY:

727060

show subpopulations

African (AFR)

AF:

0.0000896

AC:

AN:

33478

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000927

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.0000189

AC:

AN:

53042

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0000117

AC:

AN:

1112008

Other (OTH)

AF:

0.0000331

AC:

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000460

AC:

AN:

152190

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.0000241

AC:

AN:

41442

American (AMR)

AF:

0.00

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5202

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000735

AC:

AN:

68030

Other (OTH)

AF:

0.00

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000102

Hom.:

Bravo

AF:

0.0000416

ExAC

AF:

0.0000412

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Oct 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sotos syndrome

Benign:1

Apr 20, 2024

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.30

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.087

.;T;.

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.83

T;T;.

M_CAP

Uncertain

0.16

MetaRNN

Benign

0.031

T;T;T

MetaSVM

Benign

-0.28

MutationAssessor

Benign

0.46

.;N;.

PhyloP100

0.94

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.28

N;N;N

REVEL

Benign

0.11

Sift

Benign

0.092

T;T;T

Sift4G

Benign

0.073

T;T;T

Polyphen

0.068

B;B;B

Vest4

0.047

MutPred

0.18

.;Loss of phosphorylation at S2471 (P = 0.0652);.;

MVP

0.37

MPC

0.17

ClinPred

0.018

GERP RS

2.4

Varity_R

0.032

gMVP

0.10

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over