rs6038115

chr20-5280486-G-A

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 0.513 in 514,212 control chromosomes in the GnomAD database, including 68,922 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 0.52 (20476 hom., cov: 32)
  • Exomes 𝑓: 0.51 (48446 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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 (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.519 AC: 78768 AN: 151792 Hom.: 20457 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.511

GnomAD3 exomes AF: 0.516 AC: 116955 AN: 226788 Hom.: 31049 AF XY: 0.520 AC XY: 65147 AN XY: 125354

Gnomad AFR exome AF: 0.546

Gnomad AMR exome AF: 0.449

Gnomad ASJ exome AF: 0.502

Gnomad EAS exome AF: 0.675

Gnomad SAS exome AF: 0.570

Gnomad FIN exome AF: 0.526

Gnomad NFE exome AF: 0.492

Gnomad OTH exome AF: 0.497

GnomAD4 exome AF: 0.510 AC: 184860 AN: 362302 Hom.: 48446 Cov.: 0 AF XY: 0.516 AC XY: 107235 AN XY: 207826

Gnomad4 AFR exome AF: 0.547

Gnomad4 AMR exome AF: 0.448

Gnomad4 ASJ exome AF: 0.499

Gnomad4 EAS exome AF: 0.665

Gnomad4 SAS exome AF: 0.568

Gnomad4 FIN exome AF: 0.512

Gnomad4 NFE exome AF: 0.489

Gnomad4 OTH exome AF: 0.513

GnomAD4 genome AF: 0.519 AC: 78834 AN: 151910 Hom.: 20476 Cov.: 32 AF XY: 0.522 AC XY: 38725 AN XY: 74228

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.515

Alfa AF: 0.507 Hom.: 4473

Bravo AF: 0.514

Asia WGS AF: 0.601 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.4
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038115; hg19: chr20-5261132;