rs12364244

chr11-61123675-C-T

Variant summary

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

The NM_014207.4(CD5):c.1226-209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,102 control chromosomes in the GnomAD database, including 952 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 0.11 (952 hom., cov: 31)
• Consequence: CD5 NM_014207.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD5	NM_014207.4	c.1226-209C>T		intron_variant		ENST00000347785.8
CD5	NM_001346456.2	c.1055-209C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD5	ENST00000347785.8	c.1226-209C>T		intron_variant		1	NM_014207.4	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16556 AN: 151986 Hom.: 951 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.109 AC: 16572 AN: 152102 Hom.: 952 Cov.: 31 AF XY: 0.106 AC XY: 7915 AN XY: 74376

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.0597

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.103

Alfa AF: 0.119 Hom.: 134

Bravo AF: 0.112

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.17
Dann	Benign	0.60

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: rs12364244; hg19: chr11-60891147;