chr1-94824529-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001114106.3(SLC44A3):c.172G>A(p.Ala58Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,610,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A58V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001114106.3 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
SLC44A3 | NM_001114106.3 | c.172G>A | p.Ala58Thr | missense_variant | 3/15 | ENST00000271227.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A3 | ENST00000271227.11 | c.172G>A | p.Ala58Thr | missense_variant | 3/15 | 1 | NM_001114106.3 | P1 | |
SLC44A3-AS1 | ENST00000634339.1 | n.178+30715C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247234Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 133890
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1457980Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 725514
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | 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