chr9-134222034-A-G

Position:

• chr9-134222034-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 0.7 in 151,996 control chromosomes in the GnomAD database, including 38,105 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 0.70 (38105 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134222034A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106313 AN: 151878 Hom.: 38051 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.700 AC: 106431 AN: 151996 Hom.: 38105 Cov.: 31 AF XY: 0.703 AC XY: 52235 AN XY: 74284

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.744

Alfa AF: 0.638 Hom.: 31950

Bravo AF: 0.717

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11185668; hg19: chr9-137113880; COSMIC: COSV61535178;