chr3-105367463-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001627.4(ALCAM):āc.55G>Cā(p.Ala19Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001627.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALCAM | NM_001627.4 | c.55G>C | p.Ala19Pro | missense_variant | 1/16 | ENST00000306107.9 | |
ALCAM | NM_001243280.2 | c.55G>C | p.Ala19Pro | missense_variant | 1/15 | ||
ALCAM | NM_001243281.2 | c.55G>C | p.Ala19Pro | missense_variant | 1/14 | ||
ALCAM | NM_001243283.2 | c.55G>C | p.Ala19Pro | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALCAM | ENST00000306107.9 | c.55G>C | p.Ala19Pro | missense_variant | 1/16 | 1 | NM_001627.4 | A1 | |
ALCAM | ENST00000472644.6 | c.55G>C | p.Ala19Pro | missense_variant | 1/15 | 1 | P3 | ||
ALCAM | ENST00000470756.5 | n.546G>C | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248818Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134758
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461708Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727184
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at