chr11-31065144-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001387274.1(DCDC1):c.2308C>G(p.Gln770Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000809 in 759,320 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 2 hom. )
Consequence
DCDC1
NM_001387274.1 missense
NM_001387274.1 missense
Scores
10
Clinical Significance
Conservation
PhyloP100: 1.79
Genes affected
DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.011304498).
BP6
?
Variant 11-31065144-G-C is Benign according to our data. Variant chr11-31065144-G-C is described in ClinVar as [Benign]. Clinvar id is 3051102.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.2308C>G | p.Gln770Glu | missense_variant | 19/39 | ENST00000684477.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.2308C>G | p.Gln770Glu | missense_variant | 19/39 | NM_001387274.1 | A2 | ||
DCDC1 | ENST00000597505.5 | c.2308C>G | p.Gln770Glu | missense_variant | 17/36 | 5 | A2 | ||
DCDC1 | ENST00000437348.5 | n.1016C>G | non_coding_transcript_exon_variant | 9/12 | 5 | ||||
DCDC1 | ENST00000342355.8 | c.*1383C>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00262 AC: 398AN: 152088Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000605 AC: 137AN: 226480Hom.: 2 AF XY: 0.000436 AC XY: 54AN XY: 123954
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GnomAD4 exome AF: 0.000341 AC: 207AN: 607114Hom.: 2 Cov.: 0 AF XY: 0.000274 AC XY: 91AN XY: 332170
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GnomAD4 genome ? AF: 0.00267 AC: 407AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00251 AC XY: 187AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DCDC1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 13, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
PrimateAI
Benign
T
Sift4G
Benign
T
Vest4
MVP
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at