3-185514861-T-C

Variant names:

• chr3-185514861-T-C
• rs59990700
• NM_139248.3:c.983-340A>G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_139248.3(LIPH):​c.983-340A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,886 control chromosomes in the GnomAD database, including 14,154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.43 (14154 hom., cov: 31)
• Consequence: LIPH NM_139248.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.14

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 3-185514861-T-C is Benign according to our data. Variant chr3-185514861-T-C is described in ClinVar as [Benign]. Clinvar id is 1251339.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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 rank	MANE	Protein	UniProt
LIPH	NM_139248.3	c.983-340A>G		intron_variant	Intron 7 of 9	ENST00000296252.9	NP_640341.1
LIPH	XM_006713529.5	c.893-340A>G		intron_variant	Intron 6 of 8		XP_006713592.1
LIPH	XM_017005852.3	c.881-340A>G		intron_variant	Intron 6 of 8		XP_016861341.1
LIPH	XM_011512530.4	c.854-340A>G		intron_variant	Intron 8 of 10		XP_011510832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPH	ENST00000296252.9	c.983-340A>G		intron_variant	Intron 7 of 9	1	NM_139248.3	ENSP00000296252.4
LIPH	ENST00000424591.6	c.881-340A>G		intron_variant	Intron 6 of 8	1		ENSP00000396384.2
LIPH	ENST00000435679.1	c.14-340A>G		intron_variant	Intron 1 of 3	5		ENSP00000390228.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65100 AN: 151768 Hom.: 14138 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.429 AC: 65145 AN: 151886 Hom.: 14154 Cov.: 31 AF XY: 0.425 AC XY: 31579 AN XY: 74252

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.439

Alfa AF: 0.435 Hom.: 2919

Bravo AF: 0.433

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.74

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: rs59990700; hg19: chr3-185232649;