9-134483927-G-T

Variant names:

• chr9-134483927-G-T
• rs3132332

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 0.682 in 151,984 control chromosomes in the GnomAD database, including 37,040 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 0.68 (37040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.682 AC: 103615 AN: 151866 Hom.: 36981 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.683

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.682 AC: 103727 AN: 151984 Hom.: 37040 Cov.: 31 AF XY: 0.679 AC XY: 50389 AN XY: 74240

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.642

Alfa AF: 0.592 Hom.: 9700

Bravo AF: 0.684

Asia WGS AF: 0.610 AC: 2122 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	0.29
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: rs3132332; hg19: chr9-137375773;