5-141515918-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005219.5(DIAPH1):c.*933T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,318 control chromosomes in the GnomAD database, including 1,349 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005219.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH1 | ENST00000389054 | c.*933T>A | 3_prime_UTR_variant | Exon 28 of 28 | 5 | NM_005219.5 | ENSP00000373706.4 | |||
DIAPH1 | ENST00000647433 | c.*1052T>A | 3_prime_UTR_variant | Exon 29 of 29 | ENSP00000494675.1 |
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19624AN: 151104Hom.: 1350 Cov.: 32
GnomAD4 exome AF: 0.0612 AC: 6AN: 98Hom.: 0 Cov.: 0 AF XY: 0.0625 AC XY: 3AN XY: 48
GnomAD4 genome AF: 0.130 AC: 19631AN: 151220Hom.: 1349 Cov.: 32 AF XY: 0.129 AC XY: 9560AN XY: 73912
ClinVar
Submissions by phenotype
Autosomal dominant nonsyndromic hearing loss 1 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