20-43860201-A-G

Variant names:

• chr20-43860201-A-G
• rs6130470

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 0.284 in 151,904 control chromosomes in the GnomAD database, including 6,889 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 0.28 (6889 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.284 AC: 43116 AN: 151786 Hom.: 6861 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.284 AC: 43193 AN: 151904 Hom.: 6889 Cov.: 31 AF XY: 0.292 AC XY: 21652 AN XY: 74246

African (AFR) AF: 0.373 AC: 15454 AN: 41388

American (AMR) AF: 0.322 AC: 4921 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2713 AN: 5148

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4818

European-Finnish (FIN) AF: 0.174 AC: 1830 AN: 10534

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14446 AN: 67976

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.247 Hom.: 15975

Bravo AF: 0.297

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6130470; hg19: chr20-42488841;