rs56382813

Positions:

• chr10-6082294-C-T

Variant summary

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

The variant allele was found at a frequency of 0.222 in 113,700 control chromosomes in the GnomAD database, including 2,518 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 0.22 (2518 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.222 AC: 25267 AN: 113608 Hom.: 2516 Cov.: 30

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.222 AC: 25267 AN: 113700 Hom.: 2518 Cov.: 30 AF XY: 0.221 AC XY: 12237 AN XY: 55480

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.247

Alfa AF: 0.189 Hom.: 398

Bravo AF: 0.171

Asia WGS AF: 0.177 AC: 609 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56382813; hg19: chr10-6124257;