11-31257415-T-C

Position:

• chr11-31257415-T-C

Variant summary

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

The NM_001387274.1(DCDC1):​c.1054+8092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,008 control chromosomes in the GnomAD database, including 8,161 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 0.30 (8161 hom., cov: 31)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.1054+8092A>G		intron_variant		ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.1054+8092A>G		intron_variant			NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000597505.5	c.1054+8092A>G		intron_variant		5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.*35+8092A>G		intron_variant		2		ENSP00000343496.4

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45166 AN: 151890 Hom.: 8164 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.297 AC: 45166 AN: 152008 Hom.: 8161 Cov.: 31 AF XY: 0.306 AC XY: 22708 AN XY: 74296

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.282

Alfa AF: 0.331 Hom.: 1179

Bravo AF: 0.274

Asia WGS AF: 0.462 AC: 1600 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031332; hg19: chr11-31278962;