rs7902899

Variant names:

• chr10-52850672-G-A
• rs7902899

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;