2-3712240-T-C

Variant names:

• chr2-3712240-T-C
• rs6542651
• NM_001287444.2:c.339+3640T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001287444.2(DCDC2C):​c.339+3640T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,068 control chromosomes in the GnomAD database, including 9,517 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 0.26 (9517 hom., cov: 32)
• Consequence: DCDC2C NM_001287444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287444.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC2C	NM_001287444.2	MANE Select	c.339+3640T>C		intron	N/A	NP_001274373.1
	DCDC2C	NM_001365580.2		c.66+3640T>C		intron	N/A	NP_001352509.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCDC2C	ENST00000399143.9	TSL:5 MANE Select	c.339+3640T>C		intron	N/A	ENSP00000382097.4

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39280 AN: 151952 Hom.: 9472 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.259 AC: 39390 AN: 152068 Hom.: 9517 Cov.: 32 AF XY: 0.257 AC XY: 19103 AN XY: 74324

African (AFR) AF: 0.632 AC: 26207 AN: 41462

American (AMR) AF: 0.161 AC: 2462 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3466

East Asian (EAS) AF: 0.401 AC: 2070 AN: 5162

South Asian (SAS) AF: 0.0634 AC: 305 AN: 4810

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5629 AN: 68004

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.145 Hom.: 10788

Bravo AF: 0.277

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.31
PhyloP100		-0.63

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

Other links and lift over

dbSNP: rs6542651; hg19: chr2-3759830;