rs3862667

Positions:

• chr11-61107557-T-G

Variant summary

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

The NM_014207.4(CD5):​c.55+4942T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,118 control chromosomes in the GnomAD database, including 7,512 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 0.28 (7512 hom., cov: 32)
• Consequence: CD5 NM_014207.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD5	NM_014207.4	c.55+4942T>G		intron_variant		ENST00000347785.8
CD5	NM_001346456.2	c.-116-7499T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD5	ENST00000347785.8	c.55+4942T>G		intron_variant		1	NM_014207.4	P1
CD5	ENST00000544014.1	c.55+4942T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42766 AN: 152002 Hom.: 7490 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.282 AC: 42829 AN: 152118 Hom.: 7512 Cov.: 32 AF XY: 0.271 AC XY: 20146 AN XY: 74376

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.261

Alfa AF: 0.240 Hom.: 6227

Bravo AF: 0.302

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.3
DANN	Benign	0.78

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: rs3862667; hg19: chr11-60875029;