rs6038115

Variant names:

• chr20-5280486-G-A
• rs6038115

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;