rs760528892

Variant names:

• chr2-175941013-C-A
• rs760528892
• ENST00000544803.5:c.774G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-175941013-C-A
• chr2-175941013-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001305009.1(LNPK):​c.774G>T​(p.Ser258Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S258S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: LNPK NM_001305009.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

LNPK (HGNC:21610): (lunapark, ER junction formation factor) Enables identical protein binding activity. Involved in endoplasmic reticulum tubular network maintenance and positive regulation of endoplasmic reticulum tubular network organization. Located in endoplasmic reticulum tubular network membrane and nucleoplasm. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-1.36 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNPK	NM_030650.3	c.707-1356G>T		intron_variant	Intron 9 of 12	ENST00000272748.9	NP_085153.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNPK	ENST00000544803.5	c.774G>T	p.Ser258Ser	synonymous_variant	Exon 10 of 14	1		ENSP00000440905.1
LNPK	ENST00000272748.9	c.707-1356G>T		intron_variant	Intron 9 of 12	1	NM_030650.3	ENSP00000272748.4
LNPK	ENST00000409660.5	c.338-1356G>T		intron_variant	Intron 7 of 10	1		ENSP00000386237.1
LNPK	ENST00000431754.1	n.32-1356G>T		intron_variant	Intron 1 of 3	5		ENSP00000388507.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.37

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: rs760528892; hg19: chr2-176805741;