chr10-52759208-C-T

Variant names:

• chr10-52759208-C-T
• rs920727

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 0.655 in 151,938 control chromosomes in the GnomAD database, including 34,789 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 0.65 (34789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 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: 0.655 AC: 99479 AN: 151820 Hom.: 34781 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.655 AC: 99508 AN: 151938 Hom.: 34789 Cov.: 31 AF XY: 0.659 AC XY: 48894 AN XY: 74232

African (AFR) AF: 0.390 AC: 16144 AN: 41418

American (AMR) AF: 0.726 AC: 11082 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3834 AN: 5140

South Asian (SAS) AF: 0.797 AC: 3829 AN: 4806

European-Finnish (FIN) AF: 0.750 AC: 7908 AN: 10550

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51673 AN: 67966

Other (OTH) AF: 0.671 AC: 1415 AN: 2108

Alfa AF: 0.733 Hom.: 70653

Bravo AF: 0.640

Asia WGS AF: 0.761 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.79
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs920727; hg19: chr10-54518968;