chr20-50758705-A-G

Position:

• chr20-50758705-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 0.194 in 152,202 control chromosomes in the GnomAD database, including 2,945 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 0.19 (2945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.194 AC: 29491 AN: 152084 Hom.: 2944 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.194 AC: 29516 AN: 152202 Hom.: 2945 Cov.: 32 AF XY: 0.191 AC XY: 14208 AN XY: 74410

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.190

Alfa AF: 0.180 Hom.: 5648

Bravo AF: 0.200

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6122972; hg19: chr20-49375242;