rs6013897

Variant names:

• chr20-54125940-T-A
• rs6013897

Your query was ambiguous. Multiple possible variants found:

• chr20-54125940-T-A
• chr20-54125940-T-C

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 0.233 in 152,124 control chromosomes in the GnomAD database, including 4,269 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 0.23 (4269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 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: 0.233 AC: 35370 AN: 152006 Hom.: 4256 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.233 AC: 35430 AN: 152124 Hom.: 4269 Cov.: 32 AF XY: 0.234 AC XY: 17402 AN XY: 74376

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.239

Alfa AF: 0.109 Hom.: 164

Bravo AF: 0.240

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6013897; hg19: chr20-52742479;