rs11569633

Positions:

• chr20-45911096-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000372431.8(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 ENST00000372431.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLTP	NM_006227.4	c.200+56G>A		intron_variant		ENST00000372431.8	NP_006218.1
PLTP	NM_001242920.2	c.200+56G>A		intron_variant			NP_001229849.1
PLTP	NM_182676.3	c.200+56G>A		intron_variant			NP_872617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLTP	ENST00000372431.8	c.200+56G>A		intron_variant		1	NM_006227.4	ENSP00000361508	P1
PLTP	ENST00000354050.8	c.200+56G>A		intron_variant		1		ENSP00000335290
PLTP	ENST00000477313.5	c.200+56G>A		intron_variant		1		ENSP00000417138	P1
PLTP	ENST00000420868.2	c.200+56G>A		intron_variant		2		ENSP00000411671

Frequencies

GnomAD3 genomes AF: 0.00762 AC: 1160 AN: 152160 Hom.: 3 Cov.: 32

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.: 31 AF XY: 0.00983 AC XY: 7132 AN XY: 725732

Gnomad4 AFR exome AF: 0.00165

Gnomad4 AMR exome AF: 0.00383

Gnomad4 ASJ exome AF: 0.000307

Gnomad4 EAS exome AF: 0.0000756

Gnomad4 SAS exome AF: 0.00142

Gnomad4 FIN exome AF: 0.00610

Gnomad4 NFE exome AF: 0.0122

Gnomad4 OTH exome AF: 0.00834

GnomAD4 genome AF: 0.00762 AC: 1160 AN: 152278 Hom.: 3 Cov.: 32 AF XY: 0.00693 AC XY: 516 AN XY: 74460

Gnomad4 AFR AF: 0.00267

Gnomad4 AMR AF: 0.00935

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00414

Gnomad4 NFE AF: 0.0122

Gnomad4 OTH AF: 0.00710

Alfa AF: 0.00871 Hom.: 1

Bravo AF: 0.00749

Asia WGS AF: 0.000866 AC: 3 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	12
DANN	Benign	0.92

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

Other links and lift over

dbSNP: rs11569633; hg19: chr20-44539735;