rs9283880

Variant names:

• chr6-27747464-A-C
• rs9283880

Your query was ambiguous. Multiple possible variants found:

• chr6-27747464-A-C
• chr6-27747464-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;