rs6928289

Variant names:

• chr6-137352165-G-A
• rs6928289

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 0.466 in 152,080 control chromosomes in the GnomAD database, including 17,050 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 0.47 (17050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.466 AC: 70811 AN: 151962 Hom.: 17045 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.466 AC: 70856 AN: 152080 Hom.: 17050 Cov.: 33 AF XY: 0.470 AC XY: 34920 AN XY: 74328

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.469

Alfa AF: 0.430 Hom.: 3734

Bravo AF: 0.471

Asia WGS AF: 0.602 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6928289; hg19: chr6-137673302; COSMIC: COSV60284305;