9-105348449-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_080546.5(SLC44A1):c.498G>A(p.Ala166=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000661 in 1,588,488 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
NM_080546.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC44A1 | NM_080546.5 | c.498G>A | p.Ala166= | splice_region_variant, synonymous_variant | 5/16 | ENST00000374720.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC44A1 | ENST00000374720.8 | c.498G>A | p.Ala166= | splice_region_variant, synonymous_variant | 5/16 | 1 | NM_080546.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000790 AC: 12AN: 151918Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250926Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135632
GnomAD4 exome AF: 0.0000647 AC: 93AN: 1436570Hom.: 0 Cov.: 25 AF XY: 0.0000684 AC XY: 49AN XY: 716330
GnomAD4 genome AF: 0.0000790 AC: 12AN: 151918Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74188
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | SLC44A1: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at