14-100881332-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001134888.3(RTL1):c.3457G>A(p.Val1153Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,550,592 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001134888.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000316 AC: 49AN: 154972Hom.: 0 AF XY: 0.000364 AC XY: 30AN XY: 82488
GnomAD4 exome AF: 0.000129 AC: 180AN: 1398282Hom.: 1 Cov.: 88 AF XY: 0.000171 AC XY: 118AN XY: 689668
GnomAD4 genome AF: 0.000276 AC: 42AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at