chr11-6609311-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004517.4(ILK):c.631C>T(p.Arg211Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00117 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R211H) has been classified as Likely benign.
Frequency
Consequence
NM_004517.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ILK | NM_004517.4 | c.631C>T | p.Arg211Cys | missense_variant | 8/13 | ENST00000299421.9 | |
TAF10 | NM_006284.4 | c.*1611G>A | 3_prime_UTR_variant | 5/5 | ENST00000299424.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ILK | ENST00000299421.9 | c.631C>T | p.Arg211Cys | missense_variant | 8/13 | 1 | NM_004517.4 | P1 | |
TAF10 | ENST00000299424.9 | c.*1611G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_006284.4 | P1 | ||
ENST00000527398.1 | n.229-333G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 182AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000955 AC: 240AN: 251402Hom.: 0 AF XY: 0.00102 AC XY: 138AN XY: 135888
GnomAD4 exome AF: 0.00117 AC: 1710AN: 1461768Hom.: 0 Cov.: 34 AF XY: 0.00113 AC XY: 819AN XY: 727208
GnomAD4 genome AF: 0.00120 AC: 182AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 12, 2019 | The ILK c.631C>T; p.Arg211Cys variant (rs140322345) is reported in the literature in a cohort of individuals with dilated cardiomyopathy (Haas 2015). This variant is found in the Latino population with an overall allele frequency of 0.21% (74/35440 alleles) in the Genome Aggregation Database. The arginine at codon 211 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. However, given the lack of clinical and functional data, the significance of the p.Arg211Cys variant is uncertain at this time. References: Haas J et al. Atlas of the clinical genetics of human dilated cardiomyopathy. Eur Heart J. 2015 May 7;36(18):1123-35a. - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2017 | 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. - |
Primary familial hypertrophic cardiomyopathy Benign:2
Likely benign, no assertion criteria provided | clinical testing | Blueprint Genetics | Dec 20, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
ILK-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 10, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at