6-24178385-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_016356.5(DCDC2):c.1271A>C(p.Gln424Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Q424Q) has been classified as Likely benign.
Frequency
Consequence
NM_016356.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC2 | NM_016356.5 | c.1271A>C | p.Gln424Pro | missense_variant | 9/10 | ENST00000378454.8 | |
DCDC2 | NM_001195610.2 | c.1271A>C | p.Gln424Pro | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC2 | ENST00000378454.8 | c.1271A>C | p.Gln424Pro | missense_variant | 9/10 | 1 | NM_016356.5 | P1 | |
DCDC2 | ENST00000378450.6 | c.530A>C | p.Gln177Pro | missense_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nonsyndromic Deafness Pathogenic:1
Pathogenic, no assertion criteria provided | research | Centre de Biotechnologie de Sfax, Université de Sfax | Oct 01, 2014 | - - |
Autosomal recessive nonsyndromic hearing loss 66 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 18, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at