8-86217510-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138817.3(SLC7A13):c.1139G>A(p.Arg380Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,597,544 control chromosomes in the GnomAD database, including 20,846 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_138817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19709AN: 151928Hom.: 1778 Cov.: 32
GnomAD3 exomes AF: 0.181 AC: 42933AN: 237322Hom.: 4872 AF XY: 0.186 AC XY: 23937AN XY: 128546
GnomAD4 exome AF: 0.148 AC: 213757AN: 1445498Hom.: 19063 Cov.: 31 AF XY: 0.154 AC XY: 110429AN XY: 718832
GnomAD4 genome AF: 0.130 AC: 19725AN: 152046Hom.: 1783 Cov.: 32 AF XY: 0.134 AC XY: 9931AN XY: 74324
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at