rs11903032

Variant names:

• chr2-3815527-T-C
• rs11903032
• NM_001287444.2:c.1065+30427T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-3815527-T-C
• chr2-3815527-T-G

Variant summary

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

The NM_001287444.2(DCDC2C):​c.1065+30427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,162 control chromosomes in the GnomAD database, including 3,834 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 0.21 (3834 hom., cov: 33)
• Consequence: DCDC2C NM_001287444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC2C	NM_001287444.2	c.1065+30427T>C		intron_variant	Intron 10 of 10	ENST00000399143.9	NP_001274373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC2C	ENST00000399143.9	c.1065+30427T>C		intron_variant	Intron 10 of 10	5	NM_001287444.2	ENSP00000382097.4

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31806 AN: 152044 Hom.: 3831 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.209 AC: 31820 AN: 152162 Hom.: 3834 Cov.: 33 AF XY: 0.211 AC XY: 15679 AN XY: 74390

African (AFR) AF: 0.333 AC: 13831 AN: 41488

American (AMR) AF: 0.145 AC: 2223 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 347 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1483 AN: 5168

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10311 AN: 67998

Other (OTH) AF: 0.206 AC: 436 AN: 2112

Alfa AF: 0.167 Hom.: 2965

Bravo AF: 0.211

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.78
PhyloP100		0.17

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: rs11903032; hg19: chr2-3863117;