11-61120529-C-T

Variant names:

• chr11-61120529-C-T
• rs671444
• NM_014207.4:c.805+954C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014207.4(CD5):​c.805+954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,962 control chromosomes in the GnomAD database, including 12,347 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 0.39 (12347 hom., cov: 32)
• Consequence: CD5 NM_014207.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD5	NM_014207.4	c.805+954C>T		intron_variant	Intron 5 of 10	ENST00000347785.8	NP_055022.2
CD5	NM_001346456.2	c.634+954C>T		intron_variant	Intron 5 of 10		NP_001333385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD5	ENST00000347785.8	c.805+954C>T		intron_variant	Intron 5 of 10	1	NM_014207.4	ENSP00000342681.3

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58521 AN: 151844 Hom.: 12352 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.00541

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.385 AC: 58529 AN: 151962 Hom.: 12347 Cov.: 32 AF XY: 0.377 AC XY: 27976 AN XY: 74262

African (AFR) AF: 0.293 AC: 12125 AN: 41430

American (AMR) AF: 0.350 AC: 5340 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1458 AN: 3466

East Asian (EAS) AF: 0.00542 AC: 28 AN: 5168

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4822

European-Finnish (FIN) AF: 0.367 AC: 3872 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33104 AN: 67928

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.406 Hom.: 2105

Bravo AF: 0.381

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.38
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs671444; hg19: chr11-60888001;