rs6050164

Variant names:

• chr20-24934659-A-G
• rs6050164

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 0.0899 in 152,302 control chromosomes in the GnomAD database, including 698 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 0.090 (698 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 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: 0.0899 AC: 13676 AN: 152182 Hom.: 698 Cov.: 33

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0899 AC: 13693 AN: 152302 Hom.: 698 Cov.: 33 AF XY: 0.0864 AC XY: 6434 AN XY: 74490

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.0786

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0889 Hom.: 113

Bravo AF: 0.0920

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6050164; hg19: chr20-24915295;