Variant 3-185511676-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139248.3(LIPH):c.1116A>G(p.Lys372Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 1,609,114 control chromosomes in the GnomAD database, including 145,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 12707 hom., cov: 31)

Exomes 𝑓: 0.42 ( 132482 hom. )

Consequence

LIPH
NM_139248.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.266

Variant links:

Genes affected

LIPH (HGNC:18483): (lipase H) This gene encodes a membrane-bound member of the mammalian triglyceride lipase family. It catalyzes the production of 2-acyl lysophosphatidic acid (LPA), which is a lipid mediator with diverse biological properties that include platelet aggregation, smooth muscle contraction, and stimulation of cell proliferation and motility. [provided by RefSeq, Jul 2008]

LIPH links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 3-185511676-T-C is Benign according to our data. Variant chr3-185511676-T-C is described in ClinVar as [Benign]. Clinvar id is 1228610.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-185511676-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.266 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPH	NM_139248.3 linkuse as main transcript	c.1116A>G	p.Lys372Lys	synonymous_variant	9/10	ENST00000296252.9	NP_640341.1	Q8WWY8
LIPH	XM_006713529.5 linkuse as main transcript	c.1026A>G	p.Lys342Lys	synonymous_variant	8/9		XP_006713592.1
LIPH	XM_017005852.3 linkuse as main transcript	c.1014A>G	p.Lys338Lys	synonymous_variant	8/9		XP_016861341.1	A2IBA6
LIPH	XM_011512530.4 linkuse as main transcript	c.987A>G	p.Lys329Lys	synonymous_variant	10/11		XP_011510832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LIPH	ENST00000296252.9 linkuse as main transcript	c.1116A>G	p.Lys372Lys	synonymous_variant	9/10	1	NM_139248.3	ENSP00000296252.4	Q8WWY8
LIPH	ENST00000424591.6 linkuse as main transcript	c.1014A>G	p.Lys338Lys	synonymous_variant	8/9	1		ENSP00000396384.2	A2IBA6
LIPH	ENST00000435679.1 linkuse as main transcript	c.126-80A>G		intron_variant		5		ENSP00000390228.1	H7BZL3

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61461

AN:

151768

Hom.:

12697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.357

Gnomad AMI

AF:

0.564

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.452

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.445

Gnomad OTH

AF:

0.424

GnomAD3 exomes

AF:

0.397

AC:

99697

AN:

251386

Hom.:

20212

AF XY:

0.395

AC XY:

53739

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.439

Gnomad EAS exome

AF:

0.296

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.403

Gnomad NFE exome

AF:

0.452

Gnomad OTH exome

AF:

0.422

GnomAD4 exome

AF:

0.422

AC:

615654

AN:

1457228

Hom.:

132482

Cov.:

AF XY:

0.419

AC XY:

304183

AN XY:

725244

show subpopulations

Gnomad4 AFR exome

AF:

0.357

Gnomad4 AMR exome

AF:

0.371

Gnomad4 ASJ exome

AF:

0.432

Gnomad4 EAS exome

AF:

0.306

Gnomad4 SAS exome

AF:

0.287

Gnomad4 FIN exome

AF:

0.408

Gnomad4 NFE exome

AF:

0.442

Gnomad4 OTH exome

AF:

0.410

GnomAD4 genome

AF:

0.405

AC:

61490

AN:

151886

Hom.:

12707

Cov.:

AF XY:

0.402

AC XY:

29860

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.357

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.452

Gnomad4 EAS

AF:

0.298

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.415

Gnomad4 NFE

AF:

0.445

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.434

Hom.:

20525

Bravo

AF:

0.405

Asia WGS

AF:

0.311

AC:

1082

AN:

3478

EpiCase

AF:

0.447

EpiControl

AF:

0.459

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

6.5

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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