rs9283880

chr6-27747464-A-C

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 0.33 in 152,028 control chromosomes in the GnomAD database, including 9,983 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 0.33 (9983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50114 AN: 151910 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.330 AC: 50184 AN: 152028 Hom.: 9983 Cov.: 32 AF XY: 0.324 AC XY: 24105 AN XY: 74322

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.311

Alfa AF: 0.252 Hom.: 7388

Bravo AF: 0.349

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9283880; hg19: chr6-27715243; COSMIC: COSV69399382;