9-134441602-A-G

Position:

• chr9-134441602-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 0.642 in 150,408 control chromosomes in the GnomAD database, including 33,724 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 0.64 (33724 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 96615 AN: 150304 Hom.: 33734 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.642 AC: 96610 AN: 150408 Hom.: 33724 Cov.: 31 AF XY: 0.645 AC XY: 47371 AN XY: 73492

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.646

Alfa AF: 0.710 Hom.: 4839

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4842198; hg19: chr9-137333448; COSMIC: COSV62683932;