11-122871296-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019604.4(CRTAM):āc.1079A>Gā(p.Tyr360Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000012 ( 0 hom. )
Consequence
CRTAM
NM_019604.4 missense
NM_019604.4 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 3.30
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29434025).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRTAM | NM_019604.4 | c.1079A>G | p.Tyr360Cys | missense_variant | 10/10 | ENST00000227348.9 | NP_062550.2 | |
CRTAM | NM_001304782.2 | c.482A>G | p.Tyr161Cys | missense_variant | 5/5 | NP_001291711.1 | ||
CRTAM | XM_011542900.3 | c.926A>G | p.Tyr309Cys | missense_variant | 9/9 | XP_011541202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRTAM | ENST00000227348.9 | c.1079A>G | p.Tyr360Cys | missense_variant | 10/10 | 1 | NM_019604.4 | ENSP00000227348 | P1 | |
CRTAM | ENST00000533709.1 | c.482A>G | p.Tyr161Cys | missense_variant | 5/5 | 1 | ENSP00000433728 | |||
CRTAM | ENST00000533416.1 | n.391A>G | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250876Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135572
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461300Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 726930
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2023 | The c.1079A>G (p.Y360C) alteration is located in exon 10 (coding exon 10) of the CRTAM gene. This alteration results from a A to G substitution at nucleotide position 1079, causing the tyrosine (Y) at amino acid position 360 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;P
Vest4
MutPred
Gain of catalytic residue at M358 (P = 0.051);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at