Genetic Variant PLTP:c.200+56G>A (chr20-45911096-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_006227.4(PLTP):c.200+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0099 in 1,610,918 control chromosomes in the GnomAD database, including 103 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 0.0076 ( 3 hom., cov: 32)

Exomes 𝑓: 0.010 ( 100 hom. )

Consequence

PLTP
NM_006227.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.788

Variant links:

Genes affected

PLTP (HGNC:9093): (phospholipid transfer protein) The protein encoded by this gene is one of at least two lipid transfer proteins found in human plasma. The encoded protein transfers phospholipids from triglyceride-rich lipoproteins to high density lipoprotein (HDL). In addition to regulating the size of HDL particles, this protein may be involved in cholesterol metabolism. At least two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

PLTP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PLTP	NM_006227.4 link	c.200+56G>A	intron_variant	Intron 3 of 15	ENST00000372431.8	NP_006218.1	P55058-1
PLTP	NM_182676.3 link	c.200+56G>A	intron_variant	Intron 3 of 14		NP_872617.1	P55058-2
PLTP	NM_001242920.2 link	c.200+56G>A	intron_variant	Intron 3 of 13		NP_001229849.1	P55058-3
PLTP	NM_001242921.1 link	c.-290G>A	upstream_gene_variant			NP_001229850.1	P55058-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLTP	ENST00000372431.8 link	c.200+56G>A		intron_variant	Intron 3 of 15	1	NM_006227.4	ENSP00000361508.3		P55058-1

Frequencies

GnomAD3 genomes

AF:

0.00762

AC:

1160

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00268

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.00936

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00414

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0122

Gnomad OTH

AF:

0.00717

GnomAD4 exome

AF:

0.0101

AC:

14792

AN:

1458640

Hom.:

100

Cov.:

AF XY:

0.00983

AC XY:

7132

AN XY:

725732

show subpopulations

Gnomad4 AFR exome

AF:

0.00165

AC:

AN:

33420

Gnomad4 AMR exome

AF:

0.00383

AC:

171

AN:

44690

Gnomad4 ASJ exome

AF:

0.000307

AC:

AN:

26082

Gnomad4 EAS exome

AF:

0.0000756

AC:

AN:

39678

Gnomad4 SAS exome

AF:

0.00142

AC:

122

AN:

86136

Gnomad4 FIN exome

AF:

0.00610

AC:

325

AN:

53310

Gnomad4 NFE exome

AF:

0.0122

AC:

13591

AN:

1109894

Gnomad4 Remaining exome

AF:

0.00834

AC:

502

AN:

60216

Heterozygous variant carriers

828

1656

2483

3311

4139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

516

1032

1548

2064

2580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00762

AC:

1160

AN:

152278

Hom.:

Cov.:

AF XY:

0.00693

AC XY:

516

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00267

AC:

0.00267225

AN:

0.00267225

Gnomad4 AMR

AF:

0.00935

AC:

0.00935007

AN:

0.00935007

Gnomad4 ASJ

AF:

0.000288

AC:

0.000288351

AN:

0.000288351

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00166

AC:

0.001657

AN:

0.001657

Gnomad4 FIN

AF:

0.00414

AC:

0.00414079

AN:

0.00414079

Gnomad4 NFE

AF:

0.0122

AC:

0.0121729

AN:

0.0121729

Gnomad4 OTH

AF:

0.00710

AC:

0.00709555

AN:

0.00709555

Heterozygous variant carriers

108

161

215

269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00871

Hom.:

Bravo

AF:

0.00749

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.92

Mutation Taster

=98/2

polymorphism

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over