20-45174585-G-A

Variant names:

• chr20-45174585-G-A
• rs62208416

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 0.153 in 152,058 control chromosomes in the GnomAD database, including 1,907 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 0.15 (1907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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: 0.153 AC: 23193 AN: 151940 Hom.: 1902 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23232 AN: 152058 Hom.: 1907 Cov.: 32 AF XY: 0.154 AC XY: 11441 AN XY: 74338

African (AFR) AF: 0.123 AC: 5083 AN: 41470

American (AMR) AF: 0.130 AC: 1986 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3468

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5174

South Asian (SAS) AF: 0.146 AC: 701 AN: 4812

European-Finnish (FIN) AF: 0.191 AC: 2014 AN: 10560

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11836 AN: 67962

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.0912 Hom.: 124

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		-0.054
PromoterAI		-0.043	Neutral

Splicing

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

Other links and lift over

dbSNP: rs62208416; hg19: chr20-43803226;