chr3-121994196-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001199799.2(ILDR1):c.764C>T(p.Pro255Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00232 in 1,536,070 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001199799.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00355 AC: 540AN: 152150Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00268 AC: 367AN: 137134Hom.: 3 AF XY: 0.00278 AC XY: 207AN XY: 74524
GnomAD4 exome AF: 0.00219 AC: 3024AN: 1383802Hom.: 31 Cov.: 33 AF XY: 0.00209 AC XY: 1428AN XY: 682852
GnomAD4 genome AF: 0.00356 AC: 542AN: 152268Hom.: 6 Cov.: 32 AF XY: 0.00474 AC XY: 353AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
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 specified Benign:1
p.Pro255Leu in exon 6 of ILDR1: This variant is not expected to have clinical si gnificance because it has been identified in 3.3% (52/1586) of Finnish chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs144519399). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at