chr11-30931871-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001387274.1(DCDC1):āc.2797T>Cā(p.Tyr933His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000831 in 1,613,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001387274.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.2797T>C | p.Tyr933His | missense_variant | 22/39 | ENST00000684477.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.2797T>C | p.Tyr933His | missense_variant | 22/39 | NM_001387274.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000174 AC: 43AN: 247608Hom.: 0 AF XY: 0.000209 AC XY: 28AN XY: 134016
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1460914Hom.: 0 Cov.: 30 AF XY: 0.0000922 AC XY: 67AN XY: 726712
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.118T>C (p.Y40H) alteration is located in exon 3 (coding exon 2) of the DCDC5 gene. This alteration results from a T to C substitution at nucleotide position 118, causing the tyrosine (Y) at amino acid position 40 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at