6-24375322-G-A

Position:

• chr6-24375322-G-A

Variant summary

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

The NM_001195610.2(DCDC2):​c.-98+7859C>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 151,732 control chromosomes in the GnomAD database, including 23,901 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 (23901 hom., cov: 29)
• Consequence: DCDC2 NM_001195610.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

Genes affected

DCDC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCDC2	NM_001195610.2	c.-98+7859C>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: 81284 AN: 151612 Hom.: 23887 Cov.: 29

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.536 AC: 81310 AN: 151732 Hom.: 23901 Cov.: 29 AF XY: 0.541 AC XY: 40110 AN XY: 74118

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.548

Alfa AF: 0.565 Hom.: 3063

Bravo AF: 0.531

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs793694; hg19: chr6-24375550;