Variant 2-175941084-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1

The ENST00000272748.9(LNPK):c.707-1428_707-1427insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 373,318 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0045 ( 0 hom. )

Consequence

LNPK
ENST00000272748.9 intron

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.470

Variant links:

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]

LNPK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 2-175941084-C-CA is Benign according to our data. Variant chr2-175941084-C-CA is described in ClinVar as [Likely_benign]. Clinvar id is 3056562.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000327 (49/149770) while in subpopulation SAS AF= 0.000638 (3/4702). AF 95% confidence interval is 0.000209. There are 0 homozygotes in gnomad4. There are 25 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNPK	NM_030650.3 linkuse as main transcript	c.707-1428_707-1427insT		intron_variant		ENST00000272748.9	NP_085153.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
LNPK	ENST00000272748.9 linkuse as main transcript	c.707-1428_707-1427insT	intron_variant	1	NM_030650.3	ENSP00000272748	P1	Q9C0E8-1
LNPK	ENST00000409660.5 linkuse as main transcript	c.338-1428_338-1427insT	intron_variant	1		ENSP00000386237		Q9C0E8-3
LNPK	ENST00000544803.5 linkuse as main transcript	c.707-5_707-4insT	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000440905		Q9C0E8-4
LNPK	ENST00000431754.1 linkuse as main transcript	c.32-1428_32-1427insT	intron_variant, NMD_transcript_variant	5		ENSP00000388507

Frequencies

GnomAD3 genomes

AF:

0.000314

AC:

AN:

149686

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000294

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000133

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.000636

Gnomad FIN

AF:

0.000705

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000312

Gnomad OTH

AF:

0.000487

GnomAD4 exome

AF:

0.00454

AC:

1014

AN:

223548

Hom.:

Cov.:

AF XY:

0.00453

AC XY:

582

AN XY:

128574

show subpopulations

Gnomad4 AFR exome

AF:

0.00726

Gnomad4 AMR exome

AF:

0.00587

Gnomad4 ASJ exome

AF:

0.00477

Gnomad4 EAS exome

AF:

0.00820

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.00342

Gnomad4 NFE exome

AF:

0.00447

Gnomad4 OTH exome

AF:

0.00491

GnomAD4 genome

AF:

0.000327

AC:

AN:

149770

Hom.:

Cov.:

AF XY:

0.000342

AC XY:

AN XY:

73088

show subpopulations

Gnomad4 AFR

AF:

0.000318

Gnomad4 AMR

AF:

0.000199

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.000638

Gnomad4 FIN

AF:

0.000705

Gnomad4 NFE

AF:

0.000312

Gnomad4 OTH

AF:

0.000483

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

LNPK-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 22, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over