Variant chr11-35180295-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_000610.4(CD44):c.255C>T(p.His85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,613,426 control chromosomes in the GnomAD database, including 22,209 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2182 hom., cov: 31)

Exomes 𝑓: 0.16 ( 20027 hom. )

Consequence

CD44
NM_000610.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.44

Variant links:

Genes affected

CD44 (HGNC:1681): (CD44 molecule (IN blood group)) The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. [provided by RefSeq, Jul 2008]

CD44 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 11-35180295-C-T is Benign according to our data. Variant chr11-35180295-C-T is described in ClinVar as [Benign]. Clinvar id is 3059200.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD44	NM_000610.4 linkuse as main transcript	c.255C>T	p.His85=	synonymous_variant	3/18	ENST00000428726.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD44	ENST00000428726.8 linkuse as main transcript	c.255C>T	p.His85=	synonymous_variant	3/18	1	NM_000610.4	A2	P16070-1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24972

AN:

151992

Hom.:

2176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.0792

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0939

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.184

GnomAD3 exomes

AF:

0.162

AC:

40768

AN:

251238

Hom.:

3568

AF XY:

0.163

AC XY:

22143

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.209

Gnomad ASJ exome

AF:

0.244

Gnomad EAS exome

AF:

0.0811

Gnomad SAS exome

AF:

0.142

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.161

AC:

235773

AN:

1461316

Hom.:

20027

Cov.:

AF XY:

0.162

AC XY:

117637

AN XY:

727006

show subpopulations

Gnomad4 AFR exome

AF:

0.162

Gnomad4 AMR exome

AF:

0.212

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.0605

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.164

AC:

25009

AN:

152110

Hom.:

2182

Cov.:

AF XY:

0.162

AC XY:

12054

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.0796

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.0939

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.183

Alfa

AF:

0.172

Hom.:

4236

Bravo

AF:

0.172

Asia WGS

AF:

0.105

AC:

363

AN:

3478

EpiCase

AF:

0.186

EpiControl

AF:

0.189

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CD44-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

5.1

DANN

Benign

0.76

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