rs11086985

Variant names:

• chr20-45903616-A-G
• rs11086985
• NM_006227.4:c.943-1012T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006227.4(PLTP):​c.943-1012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,102 control chromosomes in the GnomAD database, including 21,926 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 0.51 (21926 hom., cov: 33)
• Consequence: PLTP NM_006227.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLTP	NM_006227.4	c.943-1012T>C		intron_variant	Intron 10 of 15	ENST00000372431.8	NP_006218.1
PLTP	NM_182676.3	c.787-1012T>C		intron_variant	Intron 9 of 14		NP_872617.1
PLTP	NM_001242921.1	c.679-1012T>C		intron_variant	Intron 8 of 13		NP_001229850.1
PLTP	NM_001242920.2	c.658-1012T>C		intron_variant	Intron 8 of 13		NP_001229849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLTP	ENST00000372431.8	c.943-1012T>C		intron_variant	Intron 10 of 15	1	NM_006227.4	ENSP00000361508.3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78109 AN: 151984 Hom.: 21921 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.514 AC: 78137 AN: 152102 Hom.: 21926 Cov.: 33 AF XY: 0.509 AC XY: 37824 AN XY: 74360

African (AFR) AF: 0.344 AC: 14282 AN: 41478

American (AMR) AF: 0.518 AC: 7909 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3466

East Asian (EAS) AF: 0.0674 AC: 349 AN: 5180

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4826

European-Finnish (FIN) AF: 0.573 AC: 6063 AN: 10572

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43509 AN: 67986

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.586 Hom.: 37275

Bravo AF: 0.495

Asia WGS AF: 0.265 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.96
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11086985; hg19: chr20-44532255;