rs9296812

Variant names:

• chr6-55926769-C-A
• rs9296812

Your query was ambiguous. Multiple possible variants found:

• chr6-55926769-C-A
• chr6-55926769-C-G

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 0.478 in 151,952 control chromosomes in the GnomAD database, including 17,934 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 0.48 (17934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.477 AC: 72457 AN: 151836 Hom.: 17894 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.478 AC: 72561 AN: 151952 Hom.: 17934 Cov.: 32 AF XY: 0.478 AC XY: 35487 AN XY: 74268

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.471

Alfa AF: 0.454 Hom.: 2636

Bravo AF: 0.488

Asia WGS AF: 0.304 AC: 1060 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	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296812; hg19: chr6-55791567;