chr9-134444068-C-G

Position:

• chr9-134444068-C-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 0.669 in 151,906 control chromosomes in the GnomAD database, including 36,108 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 0.67 (36108 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101659 AN: 151790 Hom.: 36110 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.669 AC: 101687 AN: 151906 Hom.: 36108 Cov.: 30 AF XY: 0.672 AC XY: 49878 AN XY: 74232

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.669

Alfa AF: 0.673 Hom.: 2292

Bravo AF: 0.650

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007971; hg19: chr9-137335914; COSMIC: COSV62683938;