rs9460973
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016356.5(DCDC2):c.1368A>T(p.Lys456Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 1,613,154 control chromosomes in the GnomAD database, including 8,576 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016356.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC2 | NM_016356.5 | c.1368A>T | p.Lys456Asn | missense_variant | 10/10 | ENST00000378454.8 | |
DCDC2 | NM_001195610.2 | c.1368A>T | p.Lys456Asn | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC2 | ENST00000378454.8 | c.1368A>T | p.Lys456Asn | missense_variant | 10/10 | 1 | NM_016356.5 | P1 | |
DCDC2 | ENST00000378450.6 | c.627A>T | p.Lys209Asn | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.143 AC: 21702AN: 152000Hom.: 4078 Cov.: 32
GnomAD3 exomes AF: 0.0500 AC: 12552AN: 251094Hom.: 1666 AF XY: 0.0404 AC XY: 5481AN XY: 135732
GnomAD4 exome AF: 0.0389 AC: 56887AN: 1461036Hom.: 4497 Cov.: 32 AF XY: 0.0363 AC XY: 26369AN XY: 726854
GnomAD4 genome ? AF: 0.143 AC: 21731AN: 152118Hom.: 4079 Cov.: 32 AF XY: 0.137 AC XY: 10208AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 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. - |
Autosomal recessive nonsyndromic hearing loss 66;C4479344:Isolated neonatal sclerosing cholangitis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at