chr20-18381653-C-T

Position:

• chr20-18381653-C-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 0.803 in 152,078 control chromosomes in the GnomAD database, including 49,777 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 0.80 (49777 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.803 AC: 122024 AN: 151958 Hom.: 49761 Cov.: 30

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.803 AC: 122076 AN: 152078 Hom.: 49777 Cov.: 30 AF XY: 0.806 AC XY: 59913 AN XY: 74362

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.793

Alfa AF: 0.848 Hom.: 25008

Bravo AF: 0.786

Asia WGS AF: 0.814 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2328293; hg19: chr20-18362297;