11-61109739-A-G

Position:

• chr11-61109739-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014207.4(CD5):​c.56-5317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,884 control chromosomes in the GnomAD database, including 42,479 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42479 hom., cov: 29)
• Consequence: CD5 NM_014207.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD5	NM_014207.4	c.56-5317A>G		intron_variant		ENST00000347785.8	NP_055022.2
CD5	NM_001346456.2	c.-116-5317A>G		intron_variant			NP_001333385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD5	ENST00000347785.8	c.56-5317A>G		intron_variant		1	NM_014207.4	ENSP00000342681.3
CD5	ENST00000544014.1	c.56-5317A>G		intron_variant		4		ENSP00000440899.1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111608 AN: 151766 Hom.: 42419 Cov.: 29

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.706

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.736 AC: 111735 AN: 151884 Hom.: 42479 Cov.: 29 AF XY: 0.741 AC XY: 54989 AN XY: 74214

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.710

Alfa AF: 0.564 Hom.: 1575

Bravo AF: 0.746

Asia WGS AF: 0.933 AC: 3244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.23

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

Other links and lift over

dbSNP: rs572350; hg19: chr11-60877211;