9-102433625-G-T

Position:

• chr9-102433625-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 0.0871 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.102433625G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0849

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512297; hg19: chr9-105195907;