6-137639725-A-G

Variant names:

• chr6-137639725-A-G
• rs9389526

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 0.435 in 152,090 control chromosomes in the GnomAD database, including 14,515 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 0.43 (14515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66129 AN: 151974 Hom.: 14510 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.435 AC: 66149 AN: 152090 Hom.: 14515 Cov.: 32 AF XY: 0.439 AC XY: 32641 AN XY: 74358

African (AFR) AF: 0.368 AC: 15265 AN: 41476

American (AMR) AF: 0.418 AC: 6383 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2747 AN: 5172

South Asian (SAS) AF: 0.442 AC: 2136 AN: 4830

European-Finnish (FIN) AF: 0.529 AC: 5589 AN: 10568

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31271 AN: 67984

Other (OTH) AF: 0.451 AC: 953 AN: 2114

Alfa AF: 0.319 Hom.: 921

Bravo AF: 0.423

Asia WGS AF: 0.474 AC: 1652 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	0.34
DANN	Benign	0.41
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9389526; hg19: chr6-137960862; COSMIC: COSV60285524;