rs7902899

chr10-52850672-G-A

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 0.457 in 152,034 control chromosomes in the GnomAD database, including 17,920 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 0.46 (17920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69422 AN: 151916 Hom.: 17915 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.457 AC: 69435 AN: 152034 Hom.: 17920 Cov.: 32 AF XY: 0.457 AC XY: 33953 AN XY: 74328

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.474

Alfa AF: 0.503 Hom.: 2530

Bravo AF: 0.428

Asia WGS AF: 0.539 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902899; hg19: chr10-54610432;