11-31130397-C-T

Variant names:

• chr11-31130397-C-T
• rs208068
• NM_001387274.1:c.1315-2758G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.1315-2758G>A		intron_variant	Intron 10 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.1315-2758G>A		intron_variant	Intron 10 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.1315-2758G>A		intron_variant	Intron 8 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.*390-2758G>A		intron_variant	Intron 10 of 21	2		ENSP00000343496.4
DCDC1	ENST00000534722.5	n.287-2758G>A		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85708 AN: 151844 Hom.: 25114 Cov.: 31

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.: 31 AF XY: 0.567 AC XY: 42126 AN XY: 74256

African (AFR) AF: 0.422 AC: 17492 AN: 41420

American (AMR) AF: 0.548 AC: 8366 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1852 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4793 AN: 5160

South Asian (SAS) AF: 0.689 AC: 3318 AN: 4814

European-Finnish (FIN) AF: 0.594 AC: 6284 AN: 10572

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41812 AN: 67942

Other (OTH) AF: 0.560 AC: 1183 AN: 2112

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
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs208068; hg19: chr11-31151944;