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GeneBe

1-179341109-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_003101.6(SOAT1):c.579G>A(p.Leu193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00185 in 1,614,044 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.010 ( 33 hom., cov: 32)
Exomes 𝑓: 0.00099 ( 18 hom. )

Consequence

SOAT1
NM_003101.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.856
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-179341109-G-A is Benign according to our data. Variant chr1-179341109-G-A is described in ClinVar as [Benign]. Clinvar id is 767731.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.856 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1543/152192) while in subpopulation AFR AF= 0.0352 (1462/41500). AF 95% confidence interval is 0.0337. There are 33 homozygotes in gnomad4. There are 735 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 33 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SOAT1NM_003101.6 linkuse as main transcriptc.579G>A p.Leu193= synonymous_variant 7/16 ENST00000367619.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SOAT1ENST00000367619.8 linkuse as main transcriptc.579G>A p.Leu193= synonymous_variant 7/161 NM_003101.6 P1P35610-1
SOAT1ENST00000540564.5 linkuse as main transcriptc.405G>A p.Leu135= synonymous_variant 6/151 P35610-2
SOAT1ENST00000539888.5 linkuse as main transcriptc.384G>A p.Leu128= synonymous_variant 6/152 P35610-3
SOAT1ENST00000426956.1 linkuse as main transcriptc.579G>A p.Leu193= synonymous_variant 7/73

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0100
AC:
1527
AN:
152074
Hom.:
33
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0349
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00374
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00767
GnomAD3 exomes
AF:
0.00252
AC:
634
AN:
251354
Hom.:
8
AF XY:
0.00186
AC XY:
253
AN XY:
135844
show subpopulations
Gnomad AFR exome
AF:
0.0334
Gnomad AMR exome
AF:
0.00211
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000880
Gnomad OTH exome
AF:
0.000978
GnomAD4 exome
AF:
0.000988
AC:
1445
AN:
1461852
Hom.:
18
Cov.:
31
AF XY:
0.000865
AC XY:
629
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.0336
Gnomad4 AMR exome
AF:
0.00235
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000621
Gnomad4 OTH exome
AF:
0.00224
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0101
AC:
1543
AN:
152192
Hom.:
33
Cov.:
32
AF XY:
0.00988
AC XY:
735
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0352
Gnomad4 AMR
AF:
0.00373
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00759
Alfa
AF:
0.00456
Hom.:
8
Bravo
AF:
0.0116
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
Cadd
Benign
6.4
Dann
Benign
0.81
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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.

Other links and lift over

dbSNP: rs75102484; hg19: chr1-179310244; API