5-141572026-G-A
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_005219.5(DIAPH1):c.2373C>T(p.Asp791Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,450 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 Likely benign (★★).
Frequency
Consequence
NM_005219.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Benign. The variant received -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIAPH1 | ENST00000389054.8 | c.2373C>T | p.Asp791Asp | synonymous_variant | Exon 17 of 28 | 5 | NM_005219.5 | ENSP00000373706.4 | ||
DIAPH1 | ENST00000518047.5 | c.2346C>T | p.Asp782Asp | synonymous_variant | Exon 16 of 27 | 5 | ENSP00000428268.2 | |||
DIAPH1 | ENST00000647433.1 | c.2373C>T | p.Asp791Asp | synonymous_variant | Exon 17 of 29 | ENSP00000494675.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.0000401 AC: 10AN: 249570 AF XY: 0.0000222 show subpopulations
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461450Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727078 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
p.Asp791Asp in exon 17 of DIAPH1: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 2/11566 of Latin o chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstit ute.org; dbSNP rs756608855). -
Autosomal dominant nonsyndromic hearing loss 1;C5567650:Progressive microcephaly-seizures-cortical blindness-developmental delay syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at