11-31208257-T-C

Variant names:

• chr11-31208257-T-C
• rs286651
• NM_001387274.1:c.1221+33193A>G

Variant summary

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

The NM_001387274.1(DCDC1):​c.1221+33193A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,998 control chromosomes in the GnomAD database, including 38,289 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 0.70 (38289 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.1221+33193A>G		intron_variant	Intron 9 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.1221+33193A>G		intron_variant	Intron 9 of 38		NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106201 AN: 151880 Hom.: 38233 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.699 AC: 106321 AN: 151998 Hom.: 38289 Cov.: 31 AF XY: 0.699 AC XY: 51907 AN XY: 74268

African (AFR) AF: 0.852 AC: 35344 AN: 41504

American (AMR) AF: 0.685 AC: 10458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3466

East Asian (EAS) AF: 0.956 AC: 4945 AN: 5170

South Asian (SAS) AF: 0.694 AC: 3338 AN: 4810

European-Finnish (FIN) AF: 0.595 AC: 6263 AN: 10526

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42054 AN: 67940

Other (OTH) AF: 0.665 AC: 1401 AN: 2108

Alfa AF: 0.636 Hom.: 37390

Bravo AF: 0.712

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.47
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: rs286651; hg19: chr11-31229804;