rs9332102

Variant names:

• chr10-94938199-C-A
• rs9332102

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 0.0879 in 152,144 control chromosomes in the GnomAD database, including 741 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 0.088 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0880 AC: 13371 AN: 152026 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0879 AC: 13366 AN: 152144 Hom.: 741 Cov.: 32 AF XY: 0.0866 AC XY: 6445 AN XY: 74380

African (AFR) AF: 0.0234 AC: 972 AN: 41526

American (AMR) AF: 0.0977 AC: 1493 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0392 AC: 189 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 67966

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.116 Hom.: 1378

Bravo AF: 0.0858

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.3
DANN	Benign	0.77
PhyloP100		0.024
PromoterAI		-0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9332102; hg19: chr10-96697956;