20-48172481-G-A

Variant names:

• chr20-48172481-G-A
• rs62202398

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 0.0936 in 152,092 control chromosomes in the GnomAD database, including 922 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 0.094 (922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.0936 AC: 14228 AN: 151974 Hom.: 921 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0936 AC: 14240 AN: 152092 Hom.: 922 Cov.: 32 AF XY: 0.102 AC XY: 7555 AN XY: 74340

African (AFR) AF: 0.0891 AC: 3698 AN: 41514

American (AMR) AF: 0.125 AC: 1915 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1484 AN: 5146

South Asian (SAS) AF: 0.217 AC: 1042 AN: 4808

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10576

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0584 AC: 3971 AN: 67984

Other (OTH) AF: 0.0875 AC: 185 AN: 2114

Alfa AF: 0.0713 Hom.: 890

Bravo AF: 0.0915

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.11
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs62202398; hg19: chr20-46801224;