1-219914602-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018713.3(SLC30A10):c.*847G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00338 in 152,184 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018713.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC30A10 | NM_018713.3 | c.*847G>A | 3_prime_UTR_variant | Exon 4 of 4 | ENST00000366926.4 | NP_061183.2 | ||
SLC30A10 | NM_001376929.1 | c.*847G>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001363858.1 | |||
SLC30A10 | NM_001416004.1 | c.*847G>A | 3_prime_UTR_variant | Exon 3 of 3 | NP_001402933.1 | |||
SLC30A10 | NM_001416005.1 | c.*847G>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001402934.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00338 AC: 514AN: 152066Hom.: 2 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome AF: 0.00338 AC: 514AN: 152184Hom.: 2 Cov.: 33 AF XY: 0.00352 AC XY: 262AN XY: 74394
ClinVar
Submissions by phenotype
Hypermanganesemia with dystonia, polycythemia, and cirrhosis Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at