Genetic Variant NM_022455.5:c.1482C>T (chr5-177209881-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_022455.5(NSD1):c.1482C>T(p.Cys494Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,613,566 control chromosomes in the GnomAD database, including 60,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 13160 hom., cov: 31)

Exomes 𝑓: 0.23 ( 47004 hom. )

Consequence

NSD1
NM_022455.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 1.98

Publications

37 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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 5-177209881-C-T is Benign according to our data. Variant chr5-177209881-C-T is described in ClinVar as Benign. ClinVar VariationId is 96035.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.98 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022455.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
NSD1	NM_022455.5	MANE Select	c.1482C>T	p.Cys494Cys	synonymous	Exon 5 of 23	NP_071900.2
NSD1	NM_001409301.1		c.1482C>T	p.Cys494Cys	synonymous	Exon 5 of 23	NP_001396230.1
NSD1	NM_001409302.1		c.1482C>T	p.Cys494Cys	synonymous	Exon 5 of 23	NP_001396231.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
NSD1	ENST00000439151.7	TSL:1 MANE Select	c.1482C>T	p.Cys494Cys	synonymous	Exon 5 of 23	ENSP00000395929.2
NSD1	ENST00000347982.9	TSL:1	c.609C>T	p.Cys203Cys	synonymous	Exon 6 of 24	ENSP00000343209.5
NSD1	ENST00000687453.1		c.1173C>T	p.Cys391Cys	synonymous	Exon 2 of 20	ENSP00000508426.1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54694

AN:

151792

Hom.:

13139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.315

GnomAD2 exomes

AF:

0.293

AC:

73412

AN:

250886

AF XY:

0.283

show subpopulations

Gnomad AFR exome

AF:

0.696

Gnomad AMR exome

AF:

0.301

Gnomad ASJ exome

AF:

0.205

Gnomad EAS exome

AF:

0.537

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.198

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.232

AC:

339226

AN:

1461656

Hom.:

47004

Cov.:

AF XY:

0.234

AC XY:

170003

AN XY:

727142

show subpopulations

African (AFR)

AF:

0.693

AC:

23208

AN:

33476

American (AMR)

AF:

0.297

AC:

13272

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

5417

AN:

26136

East Asian (EAS)

AF:

0.522

AC:

20703

AN:

39698

South Asian (SAS)

AF:

0.342

AC:

29507

AN:

86254

European-Finnish (FIN)

AF:

0.251

AC:

13388

AN:

53396

Middle Eastern (MID)

AF:

0.312

AC:

1798

AN:

5768

European-Non Finnish (NFE)

AF:

0.194

AC:

215807

AN:

1111820

Other (OTH)

AF:

0.267

AC:

16126

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

15036

30072

45107

60143

75179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7968

15936

23904

31872

39840

<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:

0.361

AC:

54774

AN:

151910

Hom.:

13160

Cov.:

AF XY:

0.362

AC XY:

26848

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.681

AC:

28202

AN:

41436

American (AMR)

AF:

0.285

AC:

4350

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

699

AN:

3472

East Asian (EAS)

AF:

0.527

AC:

2720

AN:

5160

South Asian (SAS)

AF:

0.364

AC:

1750

AN:

4810

European-Finnish (FIN)

AF:

0.247

AC:

2602

AN:

10534

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.200

AC:

13614

AN:

67924

Other (OTH)

AF:

0.316

AC:

664

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1499

2998

4496

5995

7494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<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:

0.251

Hom.:

10088

Bravo

AF:

0.375

Asia WGS

AF:

0.473

AC:

1640

AN:

3478

EpiCase

AF:

0.196

EpiControl

AF:

0.187

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Jun 10, 2013

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:2

Mar 03, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Inborn genetic diseases

Benign:1

Mar 19, 2016

Ambry Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Sotos syndrome

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

2.0

Mutation Taster

=100/0

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over