chr11-61123675-C-T

Variant names:

• chr11-61123675-C-T
• rs12364244
• NM_014207.4:c.1226-209C>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.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
• Publications: 1 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=-0.99).
• 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 rank	MANE	Protein	UniProt
CD5	NM_014207.4	c.1226-209C>T		intron_variant	Intron 7 of 10	ENST00000347785.8	NP_055022.2
CD5	NM_001346456.2	c.1055-209C>T		intron_variant	Intron 7 of 10		NP_001333385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD5	ENST00000347785.8	c.1226-209C>T		intron_variant	Intron 7 of 10	1	NM_014207.4	ENSP00000342681.3

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

African (AFR) AF: 0.143 AC: 5940 AN: 41478

American (AMR) AF: 0.0836 AC: 1278 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5164

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4816

European-Finnish (FIN) AF: 0.0597 AC: 634 AN: 10614

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7615 AN: 67962

Other (OTH) AF: 0.103 AC: 217 AN: 2108

Alfa AF: 0.108 Hom.: 279

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
PhyloP100		-3.5
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: rs12364244; hg19: chr11-60891147;