rs2140151

Positions:

• chr11-122866145-A-C
• chr11-122866145-A-G
• chr11-122866145-A-T

Variant summary

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

The NM_019604.4(CRTAM):​c.818-1264A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,996 control chromosomes in the GnomAD database, including 31,091 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 0.62 (31091 hom., cov: 31)
• Consequence: CRTAM NM_019604.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

CRTAM (HGNC:24313): (cytotoxic and regulatory T cell molecule) The CRTAM gene is upregulated in CD4 (see MIM 186940)-positive and CD8 (see CD8A; MIM 186910)-positive T cells and encodes a type I transmembrane protein with V and C1-like Ig domains (Yeh et al., 2008 [PubMed 18329370]).[supplied by OMIM, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRTAM	NM_019604.4	c.818-1264A>C		intron_variant		ENST00000227348.9	NP_062550.2
CRTAM	NM_001304782.2	c.221-1264A>C		intron_variant			NP_001291711.1
CRTAM	XM_011542900.3	c.665-1264A>C		intron_variant			XP_011541202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRTAM	ENST00000227348.9	c.818-1264A>C		intron_variant		1	NM_019604.4	ENSP00000227348	P1
CRTAM	ENST00000533709.1	c.221-1264A>C		intron_variant		1		ENSP00000433728
CRTAM	ENST00000533416.1	n.130-1264A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94600 AN: 151876 Hom.: 31080 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.623 AC: 94634 AN: 151996 Hom.: 31091 Cov.: 31 AF XY: 0.620 AC XY: 46065 AN XY: 74296

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.658

Alfa AF: 0.714 Hom.: 48257

Bravo AF: 0.618

Asia WGS AF: 0.515 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.96
DANN	Benign	0.82

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: rs2140151; hg19: chr11-122736853;