9-132577890-G-C

Variant names:

• chr9-132577890-G-C
• rs578802

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 0.725 in 152,148 control chromosomes in the GnomAD database, including 40,968 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 0.73 (40968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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 (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.725 AC: 110273 AN: 152030 Hom.: 40920 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.725 AC: 110380 AN: 152148 Hom.: 40968 Cov.: 32 AF XY: 0.727 AC XY: 54048 AN XY: 74370

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.720

Alfa AF: 0.555 Hom.: 1447

Bravo AF: 0.742

Asia WGS AF: 0.859 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs578802; hg19: chr9-135453277;