3-105534663-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000306107.9(ALCAM):c.548C>T(p.Ala183Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,612,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000306107.9 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALCAM | NM_001627.4 | c.548C>T | p.Ala183Val | missense_variant, splice_region_variant | 6/16 | ENST00000306107.9 | NP_001618.2 | |
ALCAM | NM_001243280.2 | c.548C>T | p.Ala183Val | missense_variant, splice_region_variant | 6/15 | NP_001230209.1 | ||
ALCAM | NM_001243281.2 | c.548C>T | p.Ala183Val | missense_variant, splice_region_variant | 6/14 | NP_001230210.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALCAM | ENST00000306107.9 | c.548C>T | p.Ala183Val | missense_variant, splice_region_variant | 6/16 | 1 | NM_001627.4 | ENSP00000305988 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 151984Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251150Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135740
GnomAD4 exome AF: 0.000106 AC: 155AN: 1460928Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 78AN XY: 726796
GnomAD4 genome AF: 0.0000855 AC: 13AN: 151984Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74206
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at