rs2877561
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001199799.2(ILDR1):c.1545T>G(p.Leu515Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,612,864 control chromosomes in the GnomAD database, including 433,612 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001199799.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.739 AC: 112440AN: 152050Hom.: 42078 Cov.: 33
GnomAD3 exomes AF: 0.726 AC: 179987AN: 247786Hom.: 66217 AF XY: 0.729 AC XY: 97823AN XY: 134202
GnomAD4 exome AF: 0.730 AC: 1066660AN: 1460696Hom.: 391494 Cov.: 59 AF XY: 0.732 AC XY: 531559AN XY: 726598
GnomAD4 genome AF: 0.740 AC: 112530AN: 152168Hom.: 42118 Cov.: 33 AF XY: 0.737 AC XY: 54851AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:4
Leu515Leu in Exon 07 of ILDR1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 28.8% (2021/7018) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2877561). -
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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. -
not provided Benign:2
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Autosomal recessive nonsyndromic hearing loss 42 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at