rs7092999

Variant names:

• chr10-100615501-G-A
• rs7092999

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;