8-86214637-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_138817.3(SLC7A13):āc.1189T>Cā(p.Ser397Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,606,100 control chromosomes in the GnomAD database, including 5 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 Likely benign (ā ).
Frequency
Consequence
NM_138817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00112 AC: 170AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000303 AC: 74AN: 244278Hom.: 0 AF XY: 0.000159 AC XY: 21AN XY: 132262
GnomAD4 exome AF: 0.000303 AC: 440AN: 1453754Hom.: 4 Cov.: 31 AF XY: 0.000313 AC XY: 226AN XY: 722590
GnomAD4 genome AF: 0.00118 AC: 180AN: 152346Hom.: 1 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at