6-80969270-G-C

Variant names:

• chr6-80969270-G-C
• rs9294188

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 0.352 in 151,792 control chromosomes in the GnomAD database, including 9,534 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 0.35 (9534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 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: 0.352 AC: 53365 AN: 151674 Hom.: 9510 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.352 AC: 53429 AN: 151792 Hom.: 9534 Cov.: 32 AF XY: 0.358 AC XY: 26522 AN XY: 74164

African (AFR) AF: 0.326 AC: 13500 AN: 41424

American (AMR) AF: 0.299 AC: 4554 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3466

East Asian (EAS) AF: 0.566 AC: 2908 AN: 5136

South Asian (SAS) AF: 0.428 AC: 2060 AN: 4814

European-Finnish (FIN) AF: 0.405 AC: 4271 AN: 10534

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23877 AN: 67880

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.206 Hom.: 443

Bravo AF: 0.342

Asia WGS AF: 0.453 AC: 1570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.69
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9294188; hg19: chr6-81678987;