chr5-177294899-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_022455.5(NSD1):c.7531G>C(p.Asp2511His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

NSD1
NM_022455.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:1

Conservation

PhyloP100: 2.81

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.12842518).

BP6

Variant 5-177294899-G-C is Benign according to our data. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729. Variant chr5-177294899-G-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 547729.

BS2

High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSD1	NM_022455.5 link	c.7531G>C	p.Asp2511His	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.7531G>C	p.Asp2511His	missense_variant	Exon 23 of 23	1	NM_022455.5	ENSP00000395929.2		Q96L73-1

Frequencies

GnomAD3 genomes

AF:

0.0000328

AC:

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000274

AC:

AN:

1461630

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727128

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33460

American (AMR)

AF:

0.0000224

AC:

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26128

East Asian (EAS)

AF:

0.00

AC:

AN:

39694

South Asian (SAS)

AF:

0.0000116

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53272

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00000180

AC:

AN:

1111954

Other (OTH)

AF:

0.00

AC:

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

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:

0.0000328

AC:

AN:

152356

Hom.:

Cov.:

AF XY:

0.0000403

AC XY:

AN XY:

74502

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41586

American (AMR)

AF:

0.000196

AC:

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000294

AC:

AN:

68038

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

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:

0.00

Hom.:

Bravo

AF:

0.00000756

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Sotos syndrome

Uncertain:2

Nov 01, 2016

Center for Human Genetics, Inc, Center for Human Genetics, Inc

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 15, 2021

Genome-Nilou Lab

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Feb 24, 2022

Labcorp Genetics (formerly Invitae), Labcorp

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

0.16

BayesDel_addAF

Benign

-0.0076

BayesDel_noAF

Benign

-0.17

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.080

.;T;.

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.36

FATHMM_MKL

Benign

0.57

LIST_S2

Benign

0.61

T;T;.

M_CAP

Pathogenic

0.38

MetaRNN

Benign

0.13

T;T;T

MetaSVM

Uncertain

0.0091

MutationAssessor

Benign

0.69

.;N;.

PhyloP100

2.8

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.78

N;N;N

REVEL

Uncertain

0.36

Sift

Uncertain

0.0010

D;D;D

Sift4G

Benign

0.094

T;T;T

Polyphen

0.51

P;B;P

Vest4

0.17

MutPred

0.097

.;Gain of MoRF binding (P = 0.0568);.;

MVP

0.50

MPC

0.55

ClinPred

0.32

GERP RS

3.9

Varity_R

0.054

gMVP

0.19

Mutation Taster

=95/5

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