11-30833358-T-G

Position:

• chr11-30833358-T-G

Variant summary

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

The ENST00000444572.6(DCDC1):​n.*410-1989A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,938 control chromosomes in the GnomAD database, including 29,314 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 0.61 (29314 hom., cov: 31)
• Consequence: DCDC1 ENST00000444572.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

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]

ENSG00000287373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984419	XR_001748485.1	n.510-1989A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000444572.6	n.*410-1989A>C		intron_variant		5		ENSP00000404672.2
ENSG00000287373	ENST00000663545.1	n.1154-14770T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92676 AN: 151820 Hom.: 29306 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.610 AC: 92718 AN: 151938 Hom.: 29314 Cov.: 31 AF XY: 0.609 AC XY: 45232 AN XY: 74260

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.658

Alfa AF: 0.681 Hom.: 70197

Bravo AF: 0.607

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015541; hg19: chr11-30854905;