rs6492706

chr13-94487130-A-G

Variant summary

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

The NM_001322186.2(DCT):c.106+17781T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,106 control chromosomes in the GnomAD database, including 35,439 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 0.68 (35439 hom., cov: 32)
• Consequence: DCT NM_001322186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

DCT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCT	NM_001322182.2	c.-338-20472T>C		intron_variant
DCT	NM_001322183.2	c.-339+2247T>C		intron_variant
DCT	NM_001322184.2	c.-639+2247T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102667 AN: 151988 Hom.: 35411 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.675 AC: 102740 AN: 152106 Hom.: 35439 Cov.: 32 AF XY: 0.672 AC XY: 49926 AN XY: 74348

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.688

Alfa AF: 0.712 Hom.: 51027

Bravo AF: 0.654

Asia WGS AF: 0.513 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.5
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6492706; hg19: chr13-95139384;