11-122867102-C-T

Position:

• chr11-122867102-C-T

Variant summary

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

The NM_019604.4(CRTAM):​c.818-307C>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

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]

CRTAM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CRTAM	NM_019604.4	c.818-307C>T		intron_variant		ENST00000227348.9	NP_062550.2
CRTAM	NM_001304782.2	c.221-307C>T		intron_variant			NP_001291711.1
CRTAM	XM_011542900.3	c.665-307C>T		intron_variant			XP_011541202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRTAM	ENST00000227348.9	c.818-307C>T		intron_variant		1	NM_019604.4	ENSP00000227348.4
CRTAM	ENST00000533709.1	c.221-307C>T		intron_variant		1		ENSP00000433728.1
CRTAM	ENST00000533416.1	n.130-307C>T		intron_variant		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

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.789

Alfa AF: 0.820 Hom.: 97668

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

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: rs7941607; hg19: chr11-122737810;