chr9-102433625-G-T

Variant names:

• chr9-102433625-G-T
• rs10512297

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 0.0871 in 152,200 control chromosomes in the GnomAD database, including 755 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 0.087 (755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 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: 0.0872 AC: 13257 AN: 152082 Hom.: 753 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0871 AC: 13264 AN: 152200 Hom.: 755 Cov.: 32 AF XY: 0.0885 AC XY: 6584 AN XY: 74410

African (AFR) AF: 0.0224 AC: 929 AN: 41556

American (AMR) AF: 0.113 AC: 1725 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.170 AC: 875 AN: 5150

South Asian (SAS) AF: 0.0735 AC: 354 AN: 4814

European-Finnish (FIN) AF: 0.124 AC: 1316 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7630 AN: 68006

Other (OTH) AF: 0.0849 AC: 179 AN: 2108

Alfa AF: 0.0976 Hom.: 130

Bravo AF: 0.0842

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.71
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10512297; hg19: chr9-105195907;