rs10988802

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.176

Alfa AF: 0.147 Hom.: 1182

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10988802; hg19: chr9-98376699;