rs1800588

chr15-58431476-C-Achr15-58431476-C-Gchr15-58431476-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The ENST00000414170(LIPC):c.-40-517C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes 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.

Frequency

Genomes: not found (cov: 31)

Consequence

LIPC
ENST00000414170 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Links

LIPC (HGNC:6619):

ALDH1A2 (HGNC:15472):

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 31.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPC	XM_005254372.2 linkuse as main transcript	c.-40-517C>A		intron_variant
LIPC	XM_024449916.2 linkuse as main transcript	c.-41+325C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Appris
LIPC	ENST00000414170.7 linkuse as main transcript	c.-40-517C>A	intron_variant	1
LIPC	ENST00000356113.10 linkuse as main transcript	c.-41+325C>A	intron_variant	2	P1
ALDH1A2	ENST00000558239.5 linkuse as main transcript	c.-306-11371G>T	intron_variant	4

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

7.4

Dann

Benign

0.49

Splicing

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over