rs163881

Variant names:

• chr11-30926697-T-G
• rs163881
• NM_001387274.1:c.2898-1289A>C

Variant summary

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

The NM_001387274.1(DCDC1):​c.2898-1289A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,106 control chromosomes in the GnomAD database, including 35,080 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 0.68 (35080 hom., cov: 33)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.2898-1289A>C		intron_variant	Intron 22 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.2898-1289A>C		intron_variant	Intron 22 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.2898-1289A>C		intron_variant	Intron 20 of 35	5		ENSP00000472625.1
DCDC1	ENST00000406071.6	c.219-1289A>C		intron_variant	Intron 3 of 19	5		ENSP00000385936.3
DCDC1	ENST00000483396.5	n.533-1289A>C		intron_variant	Intron 3 of 18	2

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102651 AN: 151988 Hom.: 35033 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.676 AC: 102752 AN: 152106 Hom.: 35080 Cov.: 33 AF XY: 0.670 AC XY: 49828 AN XY: 74358

African (AFR) AF: 0.697 AC: 28934 AN: 41502

American (AMR) AF: 0.696 AC: 10632 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2365 AN: 5172

South Asian (SAS) AF: 0.624 AC: 2998 AN: 4806

European-Finnish (FIN) AF: 0.581 AC: 6143 AN: 10570

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46427 AN: 67982

Other (OTH) AF: 0.713 AC: 1507 AN: 2114

Alfa AF: 0.681 Hom.: 5190

Bravo AF: 0.685

Asia WGS AF: 0.598 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.40
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: rs163881; hg19: chr11-30948244;