chr20-3234173-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001174089.2(SLC4A11):āc.433A>Cā(p.Arg145Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,613,864 control chromosomes in the GnomAD database, including 145,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001174089.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.485 AC: 73785AN: 151990Hom.: 18868 Cov.: 33
GnomAD3 exomes AF: 0.438 AC: 109986AN: 251272Hom.: 25175 AF XY: 0.426 AC XY: 57926AN XY: 135834
GnomAD4 exome AF: 0.411 AC: 600783AN: 1461756Hom.: 126459 Cov.: 73 AF XY: 0.408 AC XY: 296498AN XY: 727168
GnomAD4 genome AF: 0.486 AC: 73854AN: 152108Hom.: 18893 Cov.: 33 AF XY: 0.489 AC XY: 36336AN XY: 74362
ClinVar
Submissions by phenotype
Corneal dystrophy-perceptive deafness syndrome Benign:3
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Population allele frequency is 44% (rs3827075, 122,773/276,940 alleles in gnomAD v2.0.2). Based on the classification scheme RMH ACMG Guidelines v1.1.1, this variant is classified as Benign. Following criteria met: BA1 -
Congenital hereditary endothelial dystrophy of cornea Uncertain:1Benign:1
Opaque cornea with reduced visual acuity. This change was observed with the other variant (NM_032034.4:c.[2413_2414insT]). -
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not specified Benign:2
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not provided Benign:2
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Corneal dystrophy Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at