rs1547131

chr11-31365052-A-G

Variant summary

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

The NM_001387274.1(DCDC1):c.-125+4645T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,012 control chromosomes in the GnomAD database, including 6,414 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 0.29 (6414 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.-125+4645T>C		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.-125+4645T>C		intron_variant			NM_001387274.1	A2
DCDC1	ENST00000452803.1	c.-125+4645T>C		intron_variant		1		P2
DCDC1	ENST00000342355.8	c.-125+4645T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43686 AN: 151894 Hom.: 6406 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.288 AC: 43718 AN: 152012 Hom.: 6414 Cov.: 32 AF XY: 0.281 AC XY: 20873 AN XY: 74310

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.306

Alfa AF: 0.282 Hom.: 759

Bravo AF: 0.298

Asia WGS AF: 0.339 AC: 1175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.99
Dann	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547131; hg19: chr11-31386599;