dbSNP rs637186: CD5:p.His461Arg (chr11-61125134-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014207.4(CD5):c.1382A>G(p.His461Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 1,613,890 control chromosomes in the GnomAD database, including 686,879 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.94 ( 67476 hom., cov: 32)

Exomes 𝑓: 0.92 ( 619403 hom. )

Consequence

CD5
NM_014207.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.257

Variant links:

Genes affected

CD5 (HGNC:1685): (CD5 molecule) This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. This protein is a type-I transmembrane glycoprotein found on the surface of thymocytes, T lymphocytes and a subset of B lymphocytes. The encoded protein contains three SRCR domains and may act as a receptor to regulate T-cell proliferation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]

CD5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.4202916E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD5	NM_014207.4 link	c.1382A>G	p.His461Arg	missense_variant	Exon 9 of 11	ENST00000347785.8	NP_055022.2	P06127
CD5	NM_001346456.2 link	c.1211A>G	p.His404Arg	missense_variant	Exon 9 of 11		NP_001333385.1	P06127

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD5	ENST00000347785.8 link	c.1382A>G	p.His461Arg	missense_variant	Exon 9 of 11	1	NM_014207.4	ENSP00000342681.3		P06127

Frequencies

GnomAD3 genomes

AF:

0.941

AC:

143142

AN:

152136

Hom.:

67420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.983

Gnomad AMI

AF:

0.875

Gnomad AMR

AF:

0.935

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.956

Gnomad FIN

AF:

0.934

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.915

Gnomad OTH

AF:

0.933

GnomAD3 exomes

AF:

0.937

AC:

235418

AN:

251230

Hom.:

110437

AF XY:

0.934

AC XY:

126871

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.985

Gnomad AMR exome

AF:

0.961

Gnomad ASJ exome

AF:

0.901

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.950

Gnomad FIN exome

AF:

0.931

Gnomad NFE exome

AF:

0.914

Gnomad OTH exome

AF:

0.926

GnomAD4 exome

AF:

0.920

AC:

1345114

AN:

1461636

Hom.:

619403

Cov.:

AF XY:

0.921

AC XY:

669547

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.986

Gnomad4 AMR exome

AF:

0.958

Gnomad4 ASJ exome

AF:

0.904

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.951

Gnomad4 FIN exome

AF:

0.930

Gnomad4 NFE exome

AF:

0.911

Gnomad4 OTH exome

AF:

0.924

GnomAD4 genome

AF:

0.941

AC:

143257

AN:

152254

Hom.:

67476

Cov.:

AF XY:

0.942

AC XY:

70118

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.983

Gnomad4 AMR

AF:

0.935

Gnomad4 ASJ

AF:

0.905

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.955

Gnomad4 FIN

AF:

0.934

Gnomad4 NFE

AF:

0.915

Gnomad4 OTH

AF:

0.934

Alfa

AF:

0.919

Hom.:

152787

Bravo

AF:

0.943

TwinsUK

AF:

0.907

AC:

3364

ALSPAC

AF:

0.910

AC:

3509

ESP6500AA

AF:

0.984

AC:

4334

ESP6500EA

AF:

0.913

AC:

7846

ExAC

AF:

0.938

AC:

113869

Asia WGS

AF:

0.987

AC:

3433

AN:

3478

EpiCase

AF:

0.911

EpiControl

AF:

0.912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.10

DANN

Benign

0.62

DEOGEN2

Benign

0.072

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.036

MetaRNN

Benign

7.4e-7

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.11

PrimateAI

Benign

0.19

PROVEAN

Benign

-0.46

REVEL

Benign

0.051

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.0060

MPC

0.35

ClinPred

0.0049

GERP RS

-2.6

Varity_R

0.034

gMVP

0.10

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over