11-31298983-A-T

Position:

• chr11-31298983-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001387274.1(DCDC1):​c.754+6632T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,140 control chromosomes in the GnomAD database, including 32,777 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 0.65 (32777 hom., cov: 33)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.754+6632T>A		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.754+6632T>A		intron_variant			NM_001387274.1	A2
DCDC1	ENST00000452803.1	c.754+6632T>A		intron_variant		1		P2
DCDC1	ENST00000597505.5	c.754+6632T>A		intron_variant		5		A2
DCDC1	ENST00000342355.8	c.754+6632T>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99139 AN: 152024 Hom.: 32731 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.652 AC: 99243 AN: 152140 Hom.: 32777 Cov.: 33 AF XY: 0.646 AC XY: 48072 AN XY: 74378

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.685

Alfa AF: 0.640 Hom.: 3939

Bravo AF: 0.668

Asia WGS AF: 0.524 AC: 1825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2774403; hg19: chr11-31320530;