chr9-8125410-A-G

Position:

• chr9-8125410-A-G

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 0.551 in 151,916 control chromosomes in the GnomAD database, including 25,971 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 0.55 (25971 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.8125410A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83752 AN: 151798 Hom.: 25973 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.551 AC: 83759 AN: 151916 Hom.: 25971 Cov.: 32 AF XY: 0.558 AC XY: 41426 AN XY: 74218

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.547

Alfa AF: 0.659 Hom.: 44367

Bravo AF: 0.525

Asia WGS AF: 0.507 AC: 1762 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10758939; hg19: chr9-8125410; COSMIC: COSV69445996;