rs811103

Positions:

• chr6-24382669-G-A
• chr6-24382669-G-C
• chr6-24382669-G-T

Variant summary

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

The NM_001195610.2(DCDC2):​c.-98+512C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,992 control chromosomes in the GnomAD database, including 23,936 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 0.54 (23936 hom., cov: 32)
• Consequence: DCDC2 NM_001195610.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

DCDC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2	NM_001195610.2	c.-98+512C>T		intron_variant			NP_001182539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81444 AN: 151872 Hom.: 23923 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.536 AC: 81470 AN: 151992 Hom.: 23936 Cov.: 32 AF XY: 0.541 AC XY: 40210 AN XY: 74292

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.547

Alfa AF: 0.620 Hom.: 59868

Bravo AF: 0.531

Asia WGS AF: 0.708 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs811103; hg19: chr6-24382897;