rs11640439

chr16-57269282-G-Achr16-57269282-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015993.3(PLLP):c.136-7212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,166 control chromosomes in the GnomAD database, including 839 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 0.091 (839 hom., cov: 32)
• Consequence: PLLP NM_015993.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

PLLP (HGNC:18553): (plasmolipin) Predicted to be a structural constituent of myelin sheath. Predicted to be involved in myelination. Predicted to be located in compact myelin and membrane raft. Predicted to be integral component of membrane. Biomarker of schizophrenia. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLLP	NM_015993.3	c.136-7212C>T		intron_variant		ENST00000219207.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLLP	ENST00000219207.10	c.136-7212C>T		intron_variant		1	NM_015993.3	P1
PLLP	ENST00000569059.5	c.136-10698C>T		intron_variant		3
PLLP	ENST00000613167.4	c.136-7212C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13838 AN: 152048 Hom.: 839 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0910 AC: 13851 AN: 152166 Hom.: 839 Cov.: 32 AF XY: 0.0936 AC XY: 6961 AN XY: 74390

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.0864

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0834 Hom.: 568

Bravo AF: 0.0899

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.29
Dann	Benign	0.62

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: rs11640439; hg19: chr16-57303194;