chr20-48172481-G-A

Position:

• chr20-48172481-G-A

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 0.0936 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0584

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0396 Hom.: 47

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62202398; hg19: chr20-46801224;