rs7098889

Variant names:

• chr10-46051347-G-A
• rs7098889

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.452 in 151,942 control chromosomes in the GnomAD database, including 17,331 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 0.45 (17331 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 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: 0.453 AC: 68728 AN: 151824 Hom.: 17338 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.452 AC: 68720 AN: 151942 Hom.: 17331 Cov.: 31 AF XY: 0.454 AC XY: 33740 AN XY: 74252

African (AFR) AF: 0.218 AC: 9019 AN: 41444

American (AMR) AF: 0.541 AC: 8261 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2681 AN: 5146

South Asian (SAS) AF: 0.408 AC: 1963 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6448 AN: 10544

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37218 AN: 67938

Other (OTH) AF: 0.453 AC: 958 AN: 2114

Alfa AF: 0.513 Hom.: 11114

Bravo AF: 0.442

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs7098889; hg19: chr10-51544475;