Variant 16-67942789-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000264005.10(LCAT):c.428-23C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,612,138 control chromosomes in the GnomAD database, including 1,021 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.047 ( 467 hom., cov: 33)

Exomes 𝑓: 0.0093 ( 554 hom. )

Consequence

LCAT
ENST00000264005.10 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.22

Variant links:

Genes affected

LCAT (HGNC:6522): (lecithin-cholesterol acyltransferase) This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency. [provided by RefSeq, Jul 2008]

LCAT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-67942789-G-T is Benign according to our data. Variant chr16-67942789-G-T is described in ClinVar as [Benign]. Clinvar id is 1183778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCAT	NM_000229.2 linkuse as main transcript	c.428-23C>A		intron_variant		ENST00000264005.10	NP_000220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCAT	ENST00000264005.10 linkuse as main transcript	c.428-23C>A		intron_variant		1	NM_000229.2	ENSP00000264005	P1

Frequencies

GnomAD3 genomes

AF:

0.0467

AC:

7100

AN:

152180

Hom.:

463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0227

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00999

Gnomad SAS

AF:

0.0296

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00347

Gnomad OTH

AF:

0.0330

GnomAD3 exomes

AF:

0.0181

AC:

4497

AN:

248992

Hom.:

198

AF XY:

0.0165

AC XY:

2227

AN XY:

135144

show subpopulations

Gnomad AFR exome

AF:

0.150

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.00461

Gnomad EAS exome

AF:

0.00925

Gnomad SAS exome

AF:

0.0332

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00387

Gnomad OTH exome

AF:

0.0112

GnomAD4 exome

AF:

0.00931

AC:

13588

AN:

1459840

Hom.:

554

Cov.:

AF XY:

0.00939

AC XY:

6822

AN XY:

726290

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.0121

Gnomad4 ASJ exome

AF:

0.00467

Gnomad4 EAS exome

AF:

0.0114

Gnomad4 SAS exome

AF:

0.0306

Gnomad4 FIN exome

AF:

0.000421

Gnomad4 NFE exome

AF:

0.00320

Gnomad4 OTH exome

AF:

0.0159

GnomAD4 genome

AF:

0.0467

AC:

7115

AN:

152298

Hom.:

467

Cov.:

AF XY:

0.0456

AC XY:

3396

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.150

Gnomad4 AMR

AF:

0.0227

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.0100

Gnomad4 SAS

AF:

0.0294

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00347

Gnomad4 OTH

AF:

0.0327

Alfa

AF:

0.00359

Hom.:

Bravo

AF:

0.0516

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.85

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.32

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.32

Position offset: -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