chr3-121993423-G-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_001199799.2(ILDR1):c.1326C>A(p.Arg442Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,613,972 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001199799.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00262 AC: 399AN: 152200Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000620 AC: 155AN: 249962Hom.: 1 AF XY: 0.000458 AC XY: 62AN XY: 135334
GnomAD4 exome AF: 0.000276 AC: 403AN: 1461654Hom.: 1 Cov.: 41 AF XY: 0.000234 AC XY: 170AN XY: 727128
GnomAD4 genome AF: 0.00263 AC: 400AN: 152318Hom.: 1 Cov.: 33 AF XY: 0.00267 AC XY: 199AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
Arg442Arg in Exon 07 of ILDR1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 1.1% (42/3738) of Afr ican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs148350512). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at