6-129745591-A-G

Variant names:

• chr6-129745591-A-G
• rs9402168

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 0.424 in 151,996 control chromosomes in the GnomAD database, including 14,422 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 (14422 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.423 AC: 64295 AN: 151878 Hom.: 14391 Cov.: 30

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.424 AC: 64386 AN: 151996 Hom.: 14422 Cov.: 30 AF XY: 0.424 AC XY: 31475 AN XY: 74298

African (AFR) AF: 0.565 AC: 23400 AN: 41438

American (AMR) AF: 0.417 AC: 6377 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2627 AN: 5154

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10584

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23847 AN: 67940

Other (OTH) AF: 0.408 AC: 863 AN: 2114

Alfa AF: 0.370 Hom.: 18079

Bravo AF: 0.439

Asia WGS AF: 0.479 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.50
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9402168; hg19: chr6-130066736;