rs10988802

Variant names:

• chr9-95614417-G-A
• rs10988802

Your query was ambiguous. Multiple possible variants found:

• chr9-95614417-G-A
• chr9-95614417-G-T

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 0.177 in 151,958 control chromosomes in the GnomAD database, including 2,888 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 0.18 (2888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.177 AC: 26920 AN: 151838 Hom.: 2888 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.177 AC: 26941 AN: 151958 Hom.: 2888 Cov.: 32 AF XY: 0.173 AC XY: 12886 AN XY: 74322

African (AFR) AF: 0.296 AC: 12271 AN: 41400

American (AMR) AF: 0.109 AC: 1658 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3472

East Asian (EAS) AF: 0.158 AC: 817 AN: 5160

South Asian (SAS) AF: 0.156 AC: 747 AN: 4800

European-Finnish (FIN) AF: 0.0831 AC: 880 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9298 AN: 67950

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.147 Hom.: 1263

Bravo AF: 0.187

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs10988802; hg19: chr9-98376699;