11-30889444-A-C

Variant names:

• chr11-30889444-A-C
• rs273573
• NM_001387274.1:c.5082+3374T>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.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
• Publications: 8 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]

ENSG00000287373 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.5082+3374T>G		intron_variant	Intron 36 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.5082+3374T>G		intron_variant	Intron 36 of 38		NM_001387274.1	ENSP00000507427.1

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

African (AFR) AF: 0.713 AC: 29569 AN: 41450

American (AMR) AF: 0.701 AC: 10712 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5172

South Asian (SAS) AF: 0.672 AC: 3235 AN: 4812

European-Finnish (FIN) AF: 0.596 AC: 6299 AN: 10570

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

European-Non Finnish (NFE) AF: 0.685 AC: 46553 AN: 67984

Other (OTH) AF: 0.722 AC: 1520 AN: 2104

Alfa AF: 0.685 Hom.: 24225

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
PhyloP100		-1.7
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: rs273573; hg19: chr11-30910991;