dbSNP rs4651024: SOAT1:c.941+24T>C (chr1-179342967-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003101.6(SOAT1):c.941+24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 1,588,346 control chromosomes in the GnomAD database, including 188,958 homozygotes. 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: 𝑓 0.46 ( 16034 hom., cov: 31)

Exomes 𝑓: 0.49 ( 172924 hom. )

Consequence

SOAT1
NM_003101.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430

Publications

21 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003101.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SOAT1	NM_003101.6	MANE Select	c.941+24T>C	intron	N/A	NP_003092.4
SOAT1	NM_001252511.2		c.767+24T>C	intron	N/A	NP_001239440.1	P35610-2
SOAT1	NM_001252512.2		c.746+24T>C	intron	N/A	NP_001239441.1	P35610-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SOAT1	ENST00000367619.8	TSL:1 MANE Select	c.941+24T>C	intron	N/A	ENSP00000356591.3	P35610-1
SOAT1	ENST00000540564.5	TSL:1	c.767+24T>C	intron	N/A	ENSP00000445315.1	P35610-2
SOAT1	ENST00000904814.1		c.941+24T>C	intron	N/A	ENSP00000574873.1

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

69467

AN:

151820

Hom.:

16026

Cov.:

show subpopulations

Gnomad AFR

AF:

0.391

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.467

GnomAD2 exomes

AF:

0.461

AC:

115858

AN:

251142

AF XY:

0.464

show subpopulations

Gnomad AFR exome

AF:

0.386

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.417

Gnomad EAS exome

AF:

0.477

Gnomad FIN exome

AF:

0.463

Gnomad NFE exome

AF:

0.500

Gnomad OTH exome

AF:

0.476

GnomAD4 exome

AF:

0.489

AC:

702143

AN:

1436406

Hom.:

172924

Cov.:

AF XY:

0.487

AC XY:

349031

AN XY:

716352

show subpopulations

African (AFR)

AF:

0.394

AC:

12963

AN:

32882

American (AMR)

AF:

0.413

AC:

18422

AN:

44644

Ashkenazi Jewish (ASJ)

AF:

0.420

AC:

10875

AN:

25910

East Asian (EAS)

AF:

0.480

AC:

18969

AN:

39540

South Asian (SAS)

AF:

0.414

AC:

35418

AN:

85606

European-Finnish (FIN)

AF:

0.468

AC:

24957

AN:

53300

Middle Eastern (MID)

AF:

0.447

AC:

2554

AN:

5712

European-Non Finnish (NFE)

AF:

0.504

AC:

548925

AN:

1089336

Other (OTH)

AF:

0.489

AC:

29060

AN:

59476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

17370

34739

52109

69478

86848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15802

31604

47406

63208

79010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.458

AC:

69524

AN:

151940

Hom.:

16034

Cov.:

AF XY:

0.454

AC XY:

33685

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.391

AC:

16198

AN:

41408

American (AMR)

AF:

0.457

AC:

6973

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.412

AC:

1430

AN:

3472

East Asian (EAS)

AF:

0.469

AC:

2427

AN:

5172

South Asian (SAS)

AF:

0.416

AC:

2000

AN:

4812

European-Finnish (FIN)

AF:

0.458

AC:

4824

AN:

10530

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.502

AC:

34108

AN:

67978

Other (OTH)

AF:

0.471

AC:

995

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1939

3878

5816

7755

9694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.484

Hom.:

57342

Bravo

AF:

0.454

Asia WGS

AF:

0.462

AC:

1608

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.1

(source)

DANN

Benign

0.64

PhyloP100

0.043

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over