11-30905653-T-C

Variant names:

• chr11-30905653-T-C
• rs395032
• NM_001387274.1:c.4105-489A>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.4105-489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,036 control chromosomes in the GnomAD database, including 36,425 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 0.69 (36425 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 3 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]

LOC105376611 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.4105-489A>G		intron_variant	Intron 30 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.4105-489A>G		intron_variant	Intron 30 of 38		NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104527 AN: 151918 Hom.: 36369 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.688 AC: 104641 AN: 152036 Hom.: 36425 Cov.: 31 AF XY: 0.683 AC XY: 50713 AN XY: 74304

African (AFR) AF: 0.733 AC: 30414 AN: 41478

American (AMR) AF: 0.701 AC: 10700 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2376 AN: 5150

South Asian (SAS) AF: 0.668 AC: 3216 AN: 4812

European-Finnish (FIN) AF: 0.581 AC: 6142 AN: 10568

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46492 AN: 67982

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.612 Hom.: 2393

Bravo AF: 0.698

Asia WGS AF: 0.620 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.014
DANN	Benign	0.66
PhyloP100		-1.9
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: rs395032; hg19: chr11-30927200;