rs290102

Variant names:

• chr11-30993950-C-T
• rs290102
• NM_001387274.1:c.2592-41382G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):​c.2592-41382G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,880 control chromosomes in the GnomAD database, including 26,653 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 0.59 (26653 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387274.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	NM_001387274.1	MANE Select	c.2592-41382G>A		intron	N/A	NP_001374203.1
	DCDC1	NM_001367979.1		c.2592-41382G>A		intron	N/A	NP_001354908.1
	DCDC1	NR_170625.1		n.2647-41382G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC1	ENST00000684477.1	MANE Select	c.2592-41382G>A		intron	N/A	ENSP00000507427.1
	DCDC1	ENST00000597505.5	TSL:5	c.2592-41382G>A		intron	N/A	ENSP00000472625.1
	DCDC1	ENST00000342355.8	TSL:2	n.*1667-41382G>A		intron	N/A	ENSP00000343496.4

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88770 AN: 151762 Hom.: 26611 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.585 AC: 88871 AN: 151880 Hom.: 26653 Cov.: 31 AF XY: 0.577 AC XY: 42828 AN XY: 74228

African (AFR) AF: 0.692 AC: 28655 AN: 41434

American (AMR) AF: 0.520 AC: 7922 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2216 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1492 AN: 5144

South Asian (SAS) AF: 0.510 AC: 2462 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5189 AN: 10534

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38968 AN: 67926

Other (OTH) AF: 0.594 AC: 1253 AN: 2110

Alfa AF: 0.575 Hom.: 3217

Bravo AF: 0.589

Asia WGS AF: 0.433 AC: 1506 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.9
DANN	Benign	0.83
PhyloP100		-2.0
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: rs290102; hg19: chr11-31015497;