rs6025934

Variant names:

• chr20-57960806-C-T
• rs6025934

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 0.252 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.390 AC: 16186 AN: 41454

American (AMR) AF: 0.284 AC: 4347 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1222 AN: 5176

South Asian (SAS) AF: 0.190 AC: 911 AN: 4802

European-Finnish (FIN) AF: 0.214 AC: 2268 AN: 10604

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12181 AN: 67982

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.205 Hom.: 5818

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.63
DANN	Benign	0.64
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs6025934; hg19: chr20-56535862;