rs9399032

Variant names:

• chr6-132567800-T-A
• rs9399032

Your query was ambiguous. Multiple possible variants found:

• chr6-132567800-T-A
• chr6-132567800-T-C
• chr6-132567800-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.436 AC: 18066 AN: 41476

American (AMR) AF: 0.328 AC: 5010 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4085 AN: 5174

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4814

European-Finnish (FIN) AF: 0.292 AC: 3086 AN: 10572

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22025 AN: 67954

Other (OTH) AF: 0.380 AC: 803 AN: 2112

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
PhyloP100		3.1

Splicing

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

Other links and lift over

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