chr9-132370480-A-G

Position:

• chr9-132370480-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 0.887 in 152,150 control chromosomes in the GnomAD database, including 60,169 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 0.89 (60169 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.887 AC: 134893 AN: 152032 Hom.: 60139 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.887 AC: 134977 AN: 152150 Hom.: 60169 Cov.: 30 AF XY: 0.886 AC XY: 65874 AN XY: 74378

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.899

Alfa AF: 0.918 Hom.: 92221

Bravo AF: 0.882

Asia WGS AF: 0.819 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1185995; hg19: chr9-135245867;