chr11-30881290-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001387274.1(DCDC1):c.5101T>C(p.Ser1701Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,613,262 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001387274.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.5101T>C | p.Ser1701Pro | missense_variant | 37/39 | ENST00000684477.1 | |
LOC124902656 | XR_007062643.1 | n.494-5165A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.5101T>C | p.Ser1701Pro | missense_variant | 37/39 | NM_001387274.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1581AN: 152134Hom.: 33 Cov.: 33
GnomAD3 exomes AF: 0.00257 AC: 631AN: 246000Hom.: 11 AF XY: 0.00190 AC XY: 254AN XY: 133642
GnomAD4 exome AF: 0.00115 AC: 1674AN: 1461010Hom.: 33 Cov.: 30 AF XY: 0.000969 AC XY: 704AN XY: 726790
GnomAD4 genome ? AF: 0.0104 AC: 1580AN: 152252Hom.: 33 Cov.: 33 AF XY: 0.00989 AC XY: 736AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at