rs56382813

Variant names:

• chr10-6082294-C-T
• rs56382813

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;