rs9283878

Variant names:

• chr6-26754842-G-A
• rs9283878

Your query was ambiguous. Multiple possible variants found:

• chr6-26754842-G-A
• chr6-26754842-G-C
• chr6-26754842-G-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 0.0303 in 128,002 control chromosomes in the GnomAD database, including 289 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 0.030 (289 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 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: 0.0302 AC: 3868 AN: 127908 Hom.: 288 Cov.: 22

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0224

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.00261

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.00354

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0303 AC: 3878 AN: 128002 Hom.: 289 Cov.: 22 AF XY: 0.0297 AC XY: 1847 AN XY: 62086

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.0224

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.00261

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00354

Gnomad4 OTH AF: 0.0324

Alfa AF: 0.0150 Hom.: 20

Asia WGS AF: 0.0140 AC: 34 AN: 2338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9283878; hg19: chr6-26747038;