rs273573

chr11-30889444-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):c.5082+3374T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,044 control chromosomes in the GnomAD database, including 35,964 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 (35964 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.5082+3374T>G		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.5082+3374T>G		intron_variant			NM_001387274.1	A2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103944 AN: 151924 Hom.: 35911 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.684 AC: 104056 AN: 152044 Hom.: 35964 Cov.: 31 AF XY: 0.679 AC XY: 50478 AN XY: 74312

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.722

Alfa AF: 0.687 Hom.: 16447

Bravo AF: 0.692

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.8
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs273573; hg19: chr11-30910991;