6-68584593-G-A

Variant names:

• chr6-68584593-G-A
• rs9351730

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 0.418 in 151,876 control chromosomes in the GnomAD database, including 14,995 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 0.42 (14995 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63482 AN: 151762 Hom.: 14969 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.418 AC: 63533 AN: 151876 Hom.: 14995 Cov.: 33 AF XY: 0.426 AC XY: 31596 AN XY: 74232

African (AFR) AF: 0.212 AC: 8778 AN: 41428

American (AMR) AF: 0.546 AC: 8318 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4343 AN: 5150

South Asian (SAS) AF: 0.602 AC: 2905 AN: 4826

European-Finnish (FIN) AF: 0.452 AC: 4763 AN: 10526

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31572 AN: 67918

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.456 Hom.: 11335

Bravo AF: 0.418

Asia WGS AF: 0.702 AC: 2431 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9351730; hg19: chr6-69294485; COSMIC: COSV50981483;