rs968796

Positions:

• chr2-3846969-G-A
• chr2-3846969-G-C

Variant summary

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

The NM_001287444.2(DCDC2C):​c.1066-185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,050 control chromosomes in the GnomAD database, including 24,489 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 0.57 (24489 hom., cov: 32)
• Consequence: DCDC2C NM_001287444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2C	NM_001287444.2	c.1066-185G>A		intron_variant		ENST00000399143.9	NP_001274373.1
DCDC2C	NM_001365580.2	c.664-185G>A		intron_variant			NP_001352509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCDC2C	ENST00000399143.9	c.1066-185G>A		intron_variant		5	NM_001287444.2	ENSP00000382097	P1
DCDC2C	ENST00000451101.1	n.460-185G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85998 AN: 151932 Hom.: 24465 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.566 AC: 86073 AN: 152050 Hom.: 24489 Cov.: 32 AF XY: 0.570 AC XY: 42335 AN XY: 74318

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.575

Alfa AF: 0.563 Hom.: 32236

Bravo AF: 0.564

Asia WGS AF: 0.608 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.61

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: rs968796; hg19: chr2-3894559;