rs4294001

Variant names:

• chr6-50882352-G-A
• rs4294001

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 0.163 in 152,098 control chromosomes in the GnomAD database, including 2,467 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 0.16 (2467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.163 AC: 24828 AN: 151980 Hom.: 2462 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.163 AC: 24865 AN: 152098 Hom.: 2467 Cov.: 32 AF XY: 0.163 AC XY: 12127 AN XY: 74352

African (AFR) AF: 0.278 AC: 11526 AN: 41478

American (AMR) AF: 0.117 AC: 1787 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.128 AC: 660 AN: 5172

South Asian (SAS) AF: 0.124 AC: 599 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1663 AN: 10568

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7841 AN: 67990

Other (OTH) AF: 0.160 AC: 339 AN: 2114

Alfa AF: 0.125 Hom.: 707

Bravo AF: 0.163

Asia WGS AF: 0.163 AC: 565 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs4294001; hg19: chr6-50850065;