5-177294197-T-C

Position:

chr5-177294197-T-C

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_022455.5(NSD1):c.6829T>C(p.Leu2277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 1,614,048 control chromosomes in the GnomAD database, including 602,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.86 ( 57248 hom., cov: 32)

Exomes 𝑓: 0.86 ( 544869 hom. )

Consequence

NSD1
NM_022455.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.0440

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 5-177294197-T-C is Benign according to our data. Variant chr5-177294197-T-C is described in ClinVar as [Benign]. Clinvar id is 96073.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-177294197-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.044 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSD1	NM_022455.5 linkuse as main transcript	c.6829T>C	p.Leu2277=	synonymous_variant	23/23	ENST00000439151.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSD1	ENST00000439151.7 linkuse as main transcript	c.6829T>C	p.Leu2277=	synonymous_variant	23/23	1	NM_022455.5	P2	Q96L73-1

Frequencies

GnomAD3 genomes

AF:

0.863

AC:

131293

AN:

152102

Hom.:

57193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.922

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.827

Gnomad ASJ

AF:

0.886

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.753

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.877

Gnomad OTH

AF:

0.874

GnomAD3 exomes

AF:

0.819

AC:

205884

AN:

251248

Hom.:

86000

AF XY:

0.822

AC XY:

111611

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.924

Gnomad AMR exome

AF:

0.763

Gnomad ASJ exome

AF:

0.886

Gnomad EAS exome

AF:

0.481

Gnomad SAS exome

AF:

0.783

Gnomad FIN exome

AF:

0.816

Gnomad NFE exome

AF:

0.880

Gnomad OTH exome

AF:

0.847

GnomAD4 exome

AF:

0.860

AC:

1257229

AN:

1461828

Hom.:

544869

Cov.:

AF XY:

0.858

AC XY:

623843

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.930

Gnomad4 AMR exome

AF:

0.774

Gnomad4 ASJ exome

AF:

0.885

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.782

Gnomad4 FIN exome

AF:

0.814

Gnomad4 NFE exome

AF:

0.883

Gnomad4 OTH exome

AF:

0.850

GnomAD4 genome

AF:

0.863

AC:

131410

AN:

152220

Hom.:

57248

Cov.:

AF XY:

0.855

AC XY:

63635

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.923

Gnomad4 AMR

AF:

0.827

Gnomad4 ASJ

AF:

0.886

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.877

Gnomad4 OTH

AF:

0.873

Alfa

AF:

0.879

Hom.:

26581

Bravo

AF:

0.868

Asia WGS

AF:

0.666

AC:

2322

AN:

3478

EpiCase

AF:

0.884

EpiControl

AF:

0.889

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 03, 2014	- -

Sotos syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Oct 19, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 11, 2016

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.8

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over