chr11-122867102-C-T

Variant names:

• chr11-122867102-C-T
• rs7941607
• NM_019604.4:c.818-307C>T

Variant summary

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

The NM_019604.4(CRTAM):​c.818-307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,064 control chromosomes in the GnomAD database, including 43,348 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 0.75 (43348 hom., cov: 33)
• Consequence: CRTAM NM_019604.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRTAM	NM_019604.4	c.818-307C>T		intron_variant	Intron 7 of 9	ENST00000227348.9	NP_062550.2
CRTAM	NM_001304782.2	c.221-307C>T		intron_variant	Intron 2 of 4		NP_001291711.1
CRTAM	XM_011542900.3	c.665-307C>T		intron_variant	Intron 6 of 8		XP_011541202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTAM	ENST00000227348.9	c.818-307C>T		intron_variant	Intron 7 of 9	1	NM_019604.4	ENSP00000227348.4
CRTAM	ENST00000533709.1	c.221-307C>T		intron_variant	Intron 2 of 4	1		ENSP00000433728.1
CRTAM	ENST00000533416.1	n.130-307C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113546 AN: 151946 Hom.: 43327 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.747 AC: 113617 AN: 152064 Hom.: 43348 Cov.: 33 AF XY: 0.744 AC XY: 55334 AN XY: 74352

African (AFR) AF: 0.595 AC: 24636 AN: 41424

American (AMR) AF: 0.794 AC: 12120 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3132 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3226 AN: 5172

South Asian (SAS) AF: 0.764 AC: 3688 AN: 4826

European-Finnish (FIN) AF: 0.756 AC: 7994 AN: 10568

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56150 AN: 68010

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.806 Hom.: 188980

Bravo AF: 0.746

Asia WGS AF: 0.701 AC: 2436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.69
PhyloP100		0.083
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: rs7941607; hg19: chr11-122737810;