19-1397342-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000156.6(GAMT):c.*17G>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 0.0000512 in 1,602,684 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000156.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAMT | ENST00000252288 | c.*17G>A | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_000156.6 | ENSP00000252288.1 | |||
GAMT | ENST00000640762 | c.*17G>A | 3_prime_UTR_variant | Exon 6 of 6 | 5 | ENSP00000492031.1 | ||||
GAMT | ENST00000640164.1 | n.*41G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151944Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 230212Hom.: 0 AF XY: 0.0000239 AC XY: 3AN XY: 125530
GnomAD4 exome AF: 0.0000538 AC: 78AN: 1450740Hom.: 1 Cov.: 30 AF XY: 0.0000485 AC XY: 35AN XY: 721304
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151944Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74208
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at