rs6025934

chr20-57960806-C-T

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 0.252 in 152,096 control chromosomes in the GnomAD database, including 5,519 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 0.25 (5519 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38201 AN: 151976 Hom.: 5504 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.252 AC: 38261 AN: 152096 Hom.: 5519 Cov.: 31 AF XY: 0.252 AC XY: 18709 AN XY: 74358

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.270

Alfa AF: 0.198 Hom.: 4216

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.63
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6025934; hg19: chr20-56535862;