rs9388732

Variant names:

• chr6-129760128-A-C
• rs9388732

Your query was ambiguous. Multiple possible variants found:

• chr6-129760128-A-C
• chr6-129760128-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.316 in 152,026 control chromosomes in the GnomAD database, including 9,543 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 0.32 (9543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.316 AC: 48023 AN: 151908 Hom.: 9521 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.316 AC: 48083 AN: 152026 Hom.: 9543 Cov.: 32 AF XY: 0.316 AC XY: 23456 AN XY: 74336

African (AFR) AF: 0.525 AC: 21761 AN: 41444

American (AMR) AF: 0.335 AC: 5115 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2888 AN: 5156

South Asian (SAS) AF: 0.311 AC: 1495 AN: 4814

European-Finnish (FIN) AF: 0.174 AC: 1848 AN: 10596

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13099 AN: 67960

Other (OTH) AF: 0.329 AC: 695 AN: 2114

Alfa AF: 0.277 Hom.: 8035

Bravo AF: 0.342

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9388732; hg19: chr6-130081273;