rs9688660

Variant names:

• chr6-134143791-A-G
• rs9688660

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 0.347 in 152,006 control chromosomes in the GnomAD database, including 15,064 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 0.35 (15064 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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: 0.346 AC: 52585 AN: 151888 Hom.: 15015 Cov.: 30

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.347 AC: 52698 AN: 152006 Hom.: 15064 Cov.: 30 AF XY: 0.336 AC XY: 24942 AN XY: 74294

African (AFR) AF: 0.791 AC: 32782 AN: 41460

American (AMR) AF: 0.220 AC: 3368 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 723 AN: 3466

East Asian (EAS) AF: 0.0302 AC: 156 AN: 5158

South Asian (SAS) AF: 0.105 AC: 507 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1655 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12602 AN: 67952

Other (OTH) AF: 0.328 AC: 690 AN: 2106

Alfa AF: 0.271 Hom.: 2807

Bravo AF: 0.373

Asia WGS AF: 0.151 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9688660; hg19: chr6-134464929;