rs7098827

Variant names:

• chr10-131984924-G-T
• rs7098827

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 0.147 in 152,174 control chromosomes in the GnomAD database, including 1,685 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 0.15 (1685 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.147 AC: 22371 AN: 152056 Hom.: 1686 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.147 AC: 22382 AN: 152174 Hom.: 1685 Cov.: 33 AF XY: 0.146 AC XY: 10891 AN XY: 74402

African (AFR) AF: 0.130 AC: 5384 AN: 41522

American (AMR) AF: 0.137 AC: 2095 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.105 AC: 544 AN: 5174

South Asian (SAS) AF: 0.0871 AC: 420 AN: 4820

European-Finnish (FIN) AF: 0.178 AC: 1886 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10939 AN: 68002

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.158 Hom.: 5424

Bravo AF: 0.146

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7098827; hg19: chr10-133798428;