20-57853649-T-G

Position:

• chr20-57853649-T-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 0.128 in 152,230 control chromosomes in the GnomAD database, including 1,386 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 0.13 (1386 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19436 AN: 152112 Hom.: 1383 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.128 AC: 19455 AN: 152230 Hom.: 1386 Cov.: 33 AF XY: 0.134 AC XY: 9989 AN XY: 74424

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0761 Hom.: 114

Bravo AF: 0.129

Asia WGS AF: 0.260 AC: 901 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12481680; hg19: chr20-56428705;