rs6050372

Variant names:

• chr20-25152589-A-G
• rs6050372

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 0.406 in 151,768 control chromosomes in the GnomAD database, including 14,902 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 0.41 (14902 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.406 AC: 61565 AN: 151650 Hom.: 14869 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.406 AC: 61649 AN: 151768 Hom.: 14902 Cov.: 31 AF XY: 0.405 AC XY: 30033 AN XY: 74142

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.383

Alfa AF: 0.311 Hom.: 3862

Bravo AF: 0.430

Asia WGS AF: 0.443 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6050372; hg19: chr20-25133225;