rs920724

Positions:

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

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 0.698 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.724

Alfa AF: 0.688 Hom.: 2511

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920724; hg19: chr10-54532797;