6-50404289-C-T

Variant names:

• chr6-50404289-C-T
• rs2894779

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 0.29 in 151,776 control chromosomes in the GnomAD database, including 6,756 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 0.29 (6756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 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: 0.290 AC: 44024 AN: 151660 Hom.: 6758 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.290 AC: 44033 AN: 151776 Hom.: 6756 Cov.: 31 AF XY: 0.293 AC XY: 21711 AN XY: 74156

African (AFR) AF: 0.209 AC: 8639 AN: 41424

American (AMR) AF: 0.249 AC: 3792 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1184 AN: 3464

East Asian (EAS) AF: 0.482 AC: 2482 AN: 5152

South Asian (SAS) AF: 0.427 AC: 2047 AN: 4794

European-Finnish (FIN) AF: 0.318 AC: 3341 AN: 10522

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21449 AN: 67870

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.294 Hom.: 3551

Bravo AF: 0.279

Asia WGS AF: 0.435 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2894779; hg19: chr6-50372002;