6-55926769-C-A

Variant names:

• chr6-55926769-C-A
• rs9296812

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.579 AC: 23985 AN: 41428

American (AMR) AF: 0.528 AC: 8063 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3468

East Asian (EAS) AF: 0.167 AC: 864 AN: 5170

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5021 AN: 10540

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29782 AN: 67942

Other (OTH) AF: 0.471 AC: 995 AN: 2112

Alfa AF: 0.458 Hom.: 2771

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9296812; hg19: chr6-55791567;