11-61015636-C-T

Variant names:

• chr11-61015636-C-T
• rs2074229
• NM_006725.5:c.1388-77C>T

Variant summary

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

The NM_006725.5(CD6):​c.1388-77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 1,547,962 control chromosomes in the GnomAD database, including 236,968 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 0.51 (21291 hom., cov: 31)
  • Exomes 𝑓: 0.55 (215677 hom.)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 14 publications found

Genes affected

CD6 (HGNC:1691): (CD6 molecule) This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD6	NM_006725.5	c.1388-77C>T		intron_variant	Intron 8 of 12	ENST00000313421.11	NP_006716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11	c.1388-77C>T		intron_variant	Intron 8 of 12	1	NM_006725.5	ENSP00000323280.7

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78054 AN: 152008 Hom.: 21282 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.548 AC: 764938 AN: 1395836 Hom.: 215677 Cov.: 22 AF XY: 0.549 AC XY: 380192 AN XY: 692050

African (AFR) AF: 0.350 AC: 11164 AN: 31906

American (AMR) AF: 0.723 AC: 30398 AN: 42066

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 8125 AN: 24288

East Asian (EAS) AF: 0.843 AC: 32877 AN: 38988

South Asian (SAS) AF: 0.657 AC: 54498 AN: 82916

European-Finnish (FIN) AF: 0.635 AC: 33138 AN: 52180

Middle Eastern (MID) AF: 0.360 AC: 2012 AN: 5582

European-Non Finnish (NFE) AF: 0.530 AC: 562008 AN: 1060118

Other (OTH) AF: 0.532 AC: 30718 AN: 57792

GnomAD4 genome AF: 0.513 AC: 78092 AN: 152126 Hom.: 21291 Cov.: 31 AF XY: 0.525 AC XY: 39042 AN XY: 74352

African (AFR) AF: 0.360 AC: 14920 AN: 41476

American (AMR) AF: 0.640 AC: 9784 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3466

East Asian (EAS) AF: 0.836 AC: 4321 AN: 5170

South Asian (SAS) AF: 0.678 AC: 3270 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6859 AN: 10594

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36199 AN: 67984

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.518 Hom.: 18592

Bravo AF: 0.503

Asia WGS AF: 0.705 AC: 2452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.019
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: rs2074229; hg19: chr11-60783108;