rs920724

Variant names:

• chr10-52773037-G-A
• rs920724

Your query was ambiguous. Multiple possible variants found:

• chr10-52773037-G-A
• chr10-52773037-G-C

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 0.698 in 152,152 control chromosomes in the GnomAD database, including 38,753 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 0.70 (38753 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.698 AC: 106092 AN: 152032 Hom.: 38726 Cov.: 34

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.698 AC: 106167 AN: 152152 Hom.: 38753 Cov.: 34 AF XY: 0.703 AC XY: 52290 AN XY: 74392

African (AFR) AF: 0.458 AC: 19001 AN: 41454

American (AMR) AF: 0.785 AC: 12017 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2550 AN: 3462

East Asian (EAS) AF: 0.865 AC: 4468 AN: 5168

South Asian (SAS) AF: 0.754 AC: 3635 AN: 4822

European-Finnish (FIN) AF: 0.825 AC: 8752 AN: 10608

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53257 AN: 68018

Other (OTH) AF: 0.724 AC: 1531 AN: 2114

Alfa AF: 0.672 Hom.: 2597

Bravo AF: 0.686

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		-0.023
PromoterAI		0.00080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs920724; hg19: chr10-54532797;