20-23053637-T-G

Variant names:

• chr20-23053637-T-G
• rs6048519

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 0.508 in 152,016 control chromosomes in the GnomAD database, including 21,523 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 0.51 (21523 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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: 0.507 AC: 77076 AN: 151898 Hom.: 21478 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.508 AC: 77166 AN: 152016 Hom.: 21523 Cov.: 32 AF XY: 0.511 AC XY: 37999 AN XY: 74322

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.456

Alfa AF: 0.393 Hom.: 15990

Bravo AF: 0.510

Asia WGS AF: 0.452 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6048519; hg19: chr20-23034274;