rs16921914

chr11-31189224-G-Achr11-31189224-G-Cchr11-31189224-G-T

Variant summary

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

The NM_001387274.1(DCDC1):c.1222-51440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,002 control chromosomes in the GnomAD database, including 4,732 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 0.22 (4732 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.1222-51440C>T		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.1222-51440C>T		intron_variant			NM_001387274.1	A2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33726 AN: 151884 Hom.: 4735 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.222 AC: 33720 AN: 152002 Hom.: 4732 Cov.: 32 AF XY: 0.229 AC XY: 17003 AN XY: 74282

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.196

Alfa AF: 0.261 Hom.: 10817

Bravo AF: 0.201

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	9.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16921914; hg19: chr11-31210771;