Variant 11-31130397-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387274.1(DCDC1):c.1315-2758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,962 control chromosomes in the GnomAD database, including 25,119 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 25119 hom., cov: 31)

Consequence

DCDC1
NM_001387274.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.718

Variant links:

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]

DCDC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC1	NM_001387274.1 linkuse as main transcript	c.1315-2758G>A		intron_variant		ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1 linkuse as main transcript	c.1315-2758G>A	intron_variant		NM_001387274.1	ENSP00000507427	A2
DCDC1	ENST00000597505.5 linkuse as main transcript	c.1315-2758G>A	intron_variant	5		ENSP00000472625	A2	M0R2J8-1
DCDC1	ENST00000342355.8 linkuse as main transcript	c.*390-2758G>A	intron_variant, NMD_transcript_variant	2		ENSP00000343496		M0R2J8-2
DCDC1	ENST00000534722.5 linkuse as main transcript	n.287-2758G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85708

AN:

151844

Hom.:

25114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.929

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.554

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.564

AC:

85739

AN:

151962

Hom.:

25119

Cov.:

AF XY:

0.567

AC XY:

42126

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.422

Gnomad4 AMR

AF:

0.548

Gnomad4 ASJ

AF:

0.533

Gnomad4 EAS

AF:

0.929

Gnomad4 SAS

AF:

0.689

Gnomad4 FIN

AF:

0.594

Gnomad4 NFE

AF:

0.615

Gnomad4 OTH

AF:

0.560

Alfa

AF:

0.585

Hom.:

3144

Bravo

AF:

0.551

Asia WGS

AF:

0.796

AC:

2765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.47

DANN

Benign

0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over