11-122866145-A-C

Variant names:

• chr11-122866145-A-C
• rs2140151
• NM_019604.4:c.818-1264A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019604.4. 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
	CRTAM	NM_019604.4	MANE Select	c.818-1264A>C		intron	N/A	NP_062550.2
	CRTAM	NM_001304782.2		c.221-1264A>C		intron	N/A	NP_001291711.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRTAM	ENST00000227348.9	TSL:1 MANE Select	c.818-1264A>C		intron	N/A	ENSP00000227348.4
	CRTAM	ENST00000533709.1	TSL:1	c.221-1264A>C		intron	N/A	ENSP00000433728.1
	CRTAM	ENST00000533416.1	TSL:5	n.130-1264A>C		intron	N/A

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

African (AFR) AF: 0.420 AC: 17393 AN: 41434

American (AMR) AF: 0.705 AC: 10777 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2619 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2377 AN: 5158

South Asian (SAS) AF: 0.620 AC: 2989 AN: 4820

European-Finnish (FIN) AF: 0.683 AC: 7208 AN: 10558

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49143 AN: 67964

Other (OTH) AF: 0.658 AC: 1386 AN: 2106

Alfa AF: 0.704 Hom.: 60822

Bravo AF: 0.618

Asia WGS AF: 0.515 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.96
DANN	Benign	0.82
PhyloP100		0.11
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: rs2140151; hg19: chr11-122736853;