9-135348041-A-G

Position:

• chr9-135348041-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 0.395 in 151,958 control chromosomes in the GnomAD database, including 13,240 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 0.40 (13240 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135348041A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59973 AN: 151838 Hom.: 13216 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.395 AC: 60050 AN: 151958 Hom.: 13240 Cov.: 32 AF XY: 0.389 AC XY: 28917 AN XY: 74274

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.369

Alfa AF: 0.324 Hom.: 10296

Bravo AF: 0.409

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6538018; hg19: chr9-138239887;