chr20-40192165-G-T

Variant names:

• chr20-40192165-G-T
• rs6028945

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 0.109 in 152,144 control chromosomes in the GnomAD database, including 973 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 0.11 (973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 18 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 (SAS) allele frequency at 95% confidence interval = 0.176 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: 0.109 AC: 16596 AN: 152026 Hom.: 968 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.109 AC: 16613 AN: 152144 Hom.: 973 Cov.: 32 AF XY: 0.109 AC XY: 8116 AN XY: 74346

African (AFR) AF: 0.0630 AC: 2615 AN: 41516

American (AMR) AF: 0.0959 AC: 1465 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3472

East Asian (EAS) AF: 0.142 AC: 734 AN: 5174

South Asian (SAS) AF: 0.186 AC: 899 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10574

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8807 AN: 67982

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.122 Hom.: 4085

Bravo AF: 0.104

Asia WGS AF: 0.157 AC: 544 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	1.8
DANN	Benign	0.42
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6028945; hg19: chr20-38820805;