rs6048952

chr20-23626620-A-G

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 0.265 in 152,144 control chromosomes in the GnomAD database, including 6,138 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 0.27 (6136 hom., cov: 33)
  • Exomes 𝑓: 0.20 (2 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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: 0.265 AC: 40336 AN: 152006 Hom.: 6129 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.200 AC: 4 AN: 20 Hom.: 2 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.265 AC: 40371 AN: 152124 Hom.: 6136 Cov.: 33 AF XY: 0.264 AC XY: 19664 AN XY: 74380

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.239

Alfa AF: 0.227 Hom.: 4237

Bravo AF: 0.261

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.85
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6048952; hg19: chr20-23607257;