6-56050928-C-T

Position:

• chr6-56050928-C-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 0.737 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.714

Alfa AF: 0.694 Hom.: 51268

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296824; hg19: chr6-55915726;