20-50758705-A-G

Variant names:

• chr20-50758705-A-G
• rs6122972

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.247 AC: 10246 AN: 41540

American (AMR) AF: 0.191 AC: 2915 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3466

East Asian (EAS) AF: 0.129 AC: 666 AN: 5172

South Asian (SAS) AF: 0.140 AC: 675 AN: 4826

European-Finnish (FIN) AF: 0.131 AC: 1384 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12376 AN: 68004

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.184 Hom.: 12298

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6122972; hg19: chr20-49375242;