Variant chr1-179351443-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003101.6(SOAT1):c.1577A>G(p.Gln526Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0883 in 1,612,870 control chromosomes in the GnomAD database, including 8,912 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.074 ( 686 hom., cov: 31)

Exomes 𝑓: 0.090 ( 8226 hom. )

Consequence

SOAT1
NM_003101.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77

Variant links:

Genes affected

SOAT1 (HGNC:11177): (sterol O-acyltransferase 1) The protein encoded by this gene belongs to the acyltransferase family. It is located in the endoplasmic reticulum, and catalyzes the formation of fatty acid-cholesterol esters. This gene has been implicated in the formation of beta-amyloid and atherosclerotic plaques by controlling the equilibrium between free cholesterol and cytoplasmic cholesteryl esters. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]

SOAT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013990998).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOAT1	NM_003101.6 link	c.1577A>G	p.Gln526Arg	missense_variant	15/16	ENST00000367619.8	NP_003092.4	P35610-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SOAT1	ENST00000367619.8 link	c.1577A>G	p.Gln526Arg	missense_variant	15/16	1	NM_003101.6	ENSP00000356591.3	P35610-1
SOAT1	ENST00000540564.5 link	c.1403A>G	p.Gln468Arg	missense_variant	14/15	1		ENSP00000445315.1	P35610-2
SOAT1	ENST00000539888.5 link	c.1382A>G	p.Gln461Arg	missense_variant	14/15	2		ENSP00000441356.1	P35610-3

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

11236

AN:

152088

Hom.:

687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0143

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0745

Gnomad OTH

AF:

0.0631

GnomAD3 exomes

AF:

0.112

AC:

28010

AN:

250388

Hom.:

2367

AF XY:

0.111

AC XY:

14995

AN XY:

135280

show subpopulations

Gnomad AFR exome

AF:

0.0129

Gnomad AMR exome

AF:

0.170

Gnomad ASJ exome

AF:

0.0491

Gnomad EAS exome

AF:

0.328

Gnomad SAS exome

AF:

0.148

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0730

Gnomad OTH exome

AF:

0.0873

GnomAD4 exome

AF:

0.0899

AC:

131265

AN:

1460664

Hom.:

8226

Cov.:

AF XY:

0.0910

AC XY:

66148

AN XY:

726634

show subpopulations

Gnomad4 AFR exome

AF:

0.0106

Gnomad4 AMR exome

AF:

0.164

Gnomad4 ASJ exome

AF:

0.0485

Gnomad4 EAS exome

AF:

0.346

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.0989

Gnomad4 NFE exome

AF:

0.0766

Gnomad4 OTH exome

AF:

0.0873

GnomAD4 genome

AF:

0.0738

AC:

11226

AN:

152206

Hom.:

686

Cov.:

AF XY:

0.0790

AC XY:

5875

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0142

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.0493

Gnomad4 EAS

AF:

0.333

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.104

Gnomad4 NFE

AF:

0.0745

Gnomad4 OTH

AF:

0.0620

Alfa

AF:

0.0782

Hom.:

1575

Bravo

AF:

0.0723

TwinsUK

AF:

0.0801

AC:

297

ALSPAC

AF:

0.0737

AC:

284

ESP6500AA

AF:

0.0172

AC:

ESP6500EA

AF:

0.0735

AC:

632

ExAC

AF:

0.108

AC:

13072

Asia WGS

AF:

0.214

AC:

743

AN:

3478

EpiCase

AF:

0.0685

EpiControl

AF:

0.0718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.59

DEOGEN2

Benign

0.29

.;.;T

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.16

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.51

T;T;T

MetaRNN

Benign

0.0014

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.12

.;.;N

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.090

N;N;N

REVEL

Benign

0.057

Sift

Benign

0.93

T;T;T

Sift4G

Benign

0.79

T;T;T

Polyphen

0.0

.;.;B

Vest4

0.048

MPC

0.18

ClinPred

0.0083

GERP RS

5.6

Varity_R

0.061

gMVP

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over