rs7092999

chr10-100615501-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.435 in 152,104 control chromosomes in the GnomAD database, including 14,747 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 0.43 (14747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.37

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 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: 0.435 AC: 66112 AN: 151986 Hom.: 14749 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.435 AC: 66135 AN: 152104 Hom.: 14747 Cov.: 32 AF XY: 0.443 AC XY: 32913 AN XY: 74366

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.407

Alfa AF: 0.417 Hom.: 29722

Bravo AF: 0.425

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
Cadd	Uncertain	26
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7092999; hg19: chr10-102375258;