chr11-61104601-C-A

Variant names:

• chr11-61104601-C-A
• rs3862666
• NM_014207.4:c.55+1986C>A

Variant summary

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

The NM_014207.4(CD5):​c.55+1986C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,184 control chromosomes in the GnomAD database, including 4,016 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 0.22 (4016 hom., cov: 32)
• Consequence: CD5 NM_014207.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• 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 (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014207.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD5	NM_014207.4	MANE Select	c.55+1986C>A		intron	N/A	NP_055022.2
	CD5	NM_001346456.2		c.-117+10285C>A		intron	N/A	NP_001333385.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD5	ENST00000347785.8	TSL:1 MANE Select	c.55+1986C>A		intron	N/A	ENSP00000342681.3
	CD5	ENST00000544014.1	TSL:4	c.55+1986C>A		intron	N/A	ENSP00000440899.1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33425 AN: 152066 Hom.: 4008 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33452 AN: 152184 Hom.: 4016 Cov.: 32 AF XY: 0.211 AC XY: 15711 AN XY: 74388

African (AFR) AF: 0.277 AC: 11510 AN: 41516

American (AMR) AF: 0.187 AC: 2866 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3470

East Asian (EAS) AF: 0.0698 AC: 362 AN: 5184

South Asian (SAS) AF: 0.146 AC: 703 AN: 4822

European-Finnish (FIN) AF: 0.0859 AC: 912 AN: 10612

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15747 AN: 67966

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.226 Hom.: 9236

Bravo AF: 0.232

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.71
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: rs3862666; hg19: chr11-60872073;