20-45919554-C-T

Variant names:

• chr20-45919554-C-T
• rs3843763

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.347 AC: 14358 AN: 41428

American (AMR) AF: 0.189 AC: 2889 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1975 AN: 5164

South Asian (SAS) AF: 0.297 AC: 1428 AN: 4806

European-Finnish (FIN) AF: 0.258 AC: 2716 AN: 10528

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18387 AN: 67976

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.270 Hom.: 6817

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

Dec 01, 2007

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.32
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs3843763; hg19: chr20-44548193;