rs560395

chr11-31066246-A-Gchr11-31066246-A-T

Variant summary

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

The NM_001387274.1(DCDC1):c.2299-1093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,086 control chromosomes in the GnomAD database, including 23,349 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 0.54 (23349 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCDC1	NM_001387274.1	c.2299-1093T>C		intron_variant		ENST00000684477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCDC1	ENST00000684477.1	c.2299-1093T>C		intron_variant			NM_001387274.1	A2
DCDC1	ENST00000597505.5	c.2299-1093T>C		intron_variant		5		A2
DCDC1	ENST00000342355.8	c.*1374-1093T>C		intron_variant, NMD_transcript_variant		2
DCDC1	ENST00000437348.5	n.1007-1093T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81877 AN: 151968 Hom.: 23315 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.539 AC: 81963 AN: 152086 Hom.: 23349 Cov.: 32 AF XY: 0.536 AC XY: 39840 AN XY: 74338

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.544

Alfa AF: 0.518 Hom.: 3869

Bravo AF: 0.556

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.94
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560395; hg19: chr11-31087793;