20-40192165-G-T

Position:

• chr20-40192165-G-T

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 0.109 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

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 (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0630

Gnomad4 AMR AF: 0.0959

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.126

Alfa AF: 0.125 Hom.: 1961

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6028945; hg19: chr20-38820805;