rs9296812

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;