chr9-132370480-A-G

Variant names:

• chr9-132370480-A-G
• rs1185995

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;