20-45919554-C-T

Position:

• chr20-45919554-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.289 in 151,952 control chromosomes in the GnomAD database, including 6,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.29 (6508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 20-45919554-C-T is Benign according to our data. Variant chr20-45919554-C-T is described in ClinVar as [Benign]. Clinvar id is 13634.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43851 AN: 151834 Hom.: 6507 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.289 AC: 43874 AN: 151952 Hom.: 6508 Cov.: 32 AF XY: 0.286 AC XY: 21262 AN XY: 74254

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.278

Alfa AF: 0.266 Hom.: 4985

Bravo AF: 0.288

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

RECLASSIFIED - PLTP POLYMORPHISM Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Dec 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3843763; hg19: chr20-44548193;