6-137639725-A-G

Variant names:

• chr6-137639725-A-G
• rs9389526

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.435 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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.451

Alfa AF: 0.316 Hom.: 861

Bravo AF: 0.423

Asia WGS AF: 0.474 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

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