rs9399032

chr6-132567800-T-Achr6-132567800-T-Cchr6-132567800-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.372 in 152,032 control chromosomes in the GnomAD database, including 11,397 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 0.37 (11397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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: 0.372 AC: 56457 AN: 151914 Hom.: 11378 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.372 AC: 56511 AN: 152032 Hom.: 11397 Cov.: 32 AF XY: 0.374 AC XY: 27766 AN XY: 74302

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.380

Alfa AF: 0.351 Hom.: 1236

Bravo AF: 0.381

Asia WGS AF: 0.619 AC: 2149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	18
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399032; hg19: chr6-132888939; COSMIC: COSV51583028;