6-56050928-C-T

Variant names:

• chr6-56050928-C-T
• rs9296824

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 0.737 in 151,982 control chromosomes in the GnomAD database, including 41,813 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 0.74 (41813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.737 AC: 111931 AN: 151862 Hom.: 41775 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.737 AC: 112021 AN: 151982 Hom.: 41813 Cov.: 32 AF XY: 0.737 AC XY: 54777 AN XY: 74282

African (AFR) AF: 0.829 AC: 34365 AN: 41478

American (AMR) AF: 0.681 AC: 10385 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2471 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4668 AN: 5160

South Asian (SAS) AF: 0.713 AC: 3422 AN: 4802

European-Finnish (FIN) AF: 0.692 AC: 7303 AN: 10558

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47126 AN: 67948

Other (OTH) AF: 0.714 AC: 1508 AN: 2112

Alfa AF: 0.704 Hom.: 123961

Bravo AF: 0.740

Asia WGS AF: 0.789 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.42
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9296824; hg19: chr6-55915726;