chr15-84888762-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004213.5(SLC28A1):c.97-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,549,480 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_004213.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.97-10C>T | intron_variant | Intron 3 of 18 | 1 | NM_004213.5 | ENSP00000378074.1 | |||
SLC28A1 | ENST00000286749.3 | c.97-10C>T | intron_variant | Intron 2 of 17 | 1 | ENSP00000286749.3 | ||||
SLC28A1 | ENST00000338602.6 | c.97-10C>T | intron_variant | Intron 3 of 6 | 1 | ENSP00000341629.2 | ||||
SLC28A1 | ENST00000538177.5 | c.97-10C>T | intron_variant | Intron 2 of 14 | 2 | ENSP00000443752.1 |
Frequencies
GnomAD3 genomes AF: 0.00503 AC: 766AN: 152196Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00136 AC: 210AN: 154606Hom.: 2 AF XY: 0.000953 AC XY: 78AN XY: 81874
GnomAD4 exome AF: 0.000560 AC: 783AN: 1397166Hom.: 6 Cov.: 30 AF XY: 0.000453 AC XY: 312AN XY: 689408
GnomAD4 genome AF: 0.00506 AC: 770AN: 152314Hom.: 5 Cov.: 32 AF XY: 0.00485 AC XY: 361AN XY: 74472
ClinVar
Submissions by phenotype
SLC28A1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at