rs7092999

Variant names:

• chr10-100615501-G-A
• rs7092999

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.390 AC: 16175 AN: 41498

American (AMR) AF: 0.478 AC: 7307 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3528 AN: 5170

South Asian (SAS) AF: 0.544 AC: 2625 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5442 AN: 10572

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28487 AN: 67966

Other (OTH) AF: 0.407 AC: 859 AN: 2110

Alfa AF: 0.418 Hom.: 45745

Bravo AF: 0.425

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	26
DANN	Benign	0.80
PhyloP100		9.4

Splicing

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

Other links and lift over

dbSNP: rs7092999; hg19: chr10-102375258;