chr16-28985404-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001014989.2(LAT):c.95G>A(p.Arg32Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00245 in 1,613,142 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001014989.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAT | NM_001014987.2 | c.-14G>A | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000395456.7 | NP_001014987.1 | ||
LAT | NM_001014989.2 | c.95G>A | p.Arg32Gln | missense_variant | Exon 2 of 13 | NP_001014989.2 | ||
LAT | NM_014387.4 | c.-14G>A | 5_prime_UTR_variant | Exon 1 of 11 | NP_055202.1 | |||
LAT | NM_001014988.2 | c.-14G>A | 5_prime_UTR_variant | Exon 1 of 12 | NP_001014988.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0129 AC: 1956AN: 152146Hom.: 42 Cov.: 32
GnomAD3 exomes AF: 0.00347 AC: 870AN: 250448Hom.: 24 AF XY: 0.00234 AC XY: 317AN XY: 135432
GnomAD4 exome AF: 0.00136 AC: 1993AN: 1460878Hom.: 38 Cov.: 33 AF XY: 0.00117 AC XY: 849AN XY: 726766
GnomAD4 genome AF: 0.0129 AC: 1958AN: 152264Hom.: 42 Cov.: 32 AF XY: 0.0125 AC XY: 934AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at