20-46005181-A-G

Variant names:

• chr20-46005181-A-G
• rs3848722

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 0.454 in 151,566 control chromosomes in the GnomAD database, including 16,869 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 0.45 (16869 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.454 AC: 68763 AN: 151448 Hom.: 16843 Cov.: 30

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.454 AC: 68829 AN: 151566 Hom.: 16869 Cov.: 30 AF XY: 0.459 AC XY: 33992 AN XY: 74014

African (AFR) AF: 0.623 AC: 25735 AN: 41334

American (AMR) AF: 0.306 AC: 4644 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3736 AN: 5138

South Asian (SAS) AF: 0.525 AC: 2520 AN: 4804

European-Finnish (FIN) AF: 0.449 AC: 4712 AN: 10486

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24830 AN: 67826

Other (OTH) AF: 0.407 AC: 858 AN: 2108

Alfa AF: 0.422 Hom.: 1814

Bravo AF: 0.450

Asia WGS AF: 0.573 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3848722; hg19: chr20-44633820;