rs11677370

Positions:

• chr2-3793830-T-A
• chr2-3793830-T-G

Variant summary

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

The NM_001287444.2(DCDC2C):​c.1065+8730T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,026 control chromosomes in the GnomAD database, including 9,078 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 0.34 (9078 hom., cov: 33)
• Consequence: DCDC2C NM_001287444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

Genes affected

DCDC2C (HGNC:32696): (doublecortin domain containing 2C) Predicted to be involved in intracellular signal transduction. Located in cytoplasm and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

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 (SAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2C	NM_001287444.2	c.1065+8730T>A		intron_variant		ENST00000399143.9	NP_001274373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC2C	ENST00000399143.9	c.1065+8730T>A		intron_variant		5	NM_001287444.2	ENSP00000382097	P1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51561 AN: 151908 Hom.: 9070 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.339 AC: 51611 AN: 152026 Hom.: 9078 Cov.: 33 AF XY: 0.350 AC XY: 26022 AN XY: 74304

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.336

Alfa AF: 0.202 Hom.: 475

Bravo AF: 0.327

Asia WGS AF: 0.462 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.58

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: rs11677370; hg19: chr2-3841420; COSMIC: COSV68616491;