6-27260480-G-A

Variant names:

• chr6-27260480-G-A
• rs9348756

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 0.0653 in 152,154 control chromosomes in the GnomAD database, including 582 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 0.065 (582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.0833 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: 0.0653 AC: 9934 AN: 152036 Hom.: 583 Cov.: 31

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0653 AC: 9932 AN: 152154 Hom.: 582 Cov.: 31 AF XY: 0.0697 AC XY: 5187 AN XY: 74380

African (AFR) AF: 0.0137 AC: 570 AN: 41514

American (AMR) AF: 0.0375 AC: 573 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.0612 AC: 316 AN: 5166

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10566

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0851 AC: 5787 AN: 68004

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0377 Hom.: 33

Bravo AF: 0.0504

Asia WGS AF: 0.0290 AC: 102 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	1.4
DANN	Benign	0.84
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9348756; hg19: chr6-27228259;