rs9332092

Variant names:

• chr10-94936772-T-C
• rs9332092

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 0.0494 in 152,240 control chromosomes in the GnomAD database, including 245 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 0.049 (245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0495 AC: 7534 AN: 152122 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0494 AC: 7527 AN: 152240 Hom.: 245 Cov.: 32 AF XY: 0.0500 AC XY: 3722 AN XY: 74442

African (AFR) AF: 0.0125 AC: 521 AN: 41556

American (AMR) AF: 0.0491 AC: 751 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5176

South Asian (SAS) AF: 0.114 AC: 551 AN: 4818

European-Finnish (FIN) AF: 0.0557 AC: 591 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4507 AN: 68006

Other (OTH) AF: 0.0520 AC: 110 AN: 2116

Alfa AF: 0.0601 Hom.: 357

Bravo AF: 0.0462

Asia WGS AF: 0.0760 AC: 266 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.48
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9332092; hg19: chr10-96696529;