rs4294001

Variant names:

• chr6-50882352-G-A
• rs4294001

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 0.163 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.160

Alfa AF: 0.125 Hom.: 648

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4294001; hg19: chr6-50850065;