rs56382813

Variant names:

• chr10-6082294-C-T
• rs56382813

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0736 AC: 2746 AN: 37332

American (AMR) AF: 0.296 AC: 3314 AN: 11210

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 596 AN: 2264

East Asian (EAS) AF: 0.235 AC: 1102 AN: 4696

South Asian (SAS) AF: 0.249 AC: 661 AN: 2658

European-Finnish (FIN) AF: 0.246 AC: 1805 AN: 7326

Middle Eastern (MID) AF: 0.244 AC: 43 AN: 176

European-Non Finnish (NFE) AF: 0.316 AC: 14512 AN: 45948

Other (OTH) AF: 0.247 AC: 356 AN: 1440

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.18
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs56382813; hg19: chr10-6124257;