1-179298648-G-T

Variant names:

• chr1-179298648-G-T
• rs2265932
• NM_003101.6:c.-8-4029G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003101.6(SOAT1):​c.-8-4029G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,054 control chromosomes in the GnomAD database, including 45,942 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 0.78 (45942 hom., cov: 31)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.-8-4029G>T		intron_variant	Intron 1 of 15	ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.-8-4029G>T		intron_variant	Intron 1 of 15	1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.-123-4029G>T		intron_variant	Intron 1 of 14	1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.-78+4712G>T		intron_variant	Intron 1 of 14	2		ENSP00000441356.1
SOAT1	ENST00000426956.1	c.-8-4029G>T		intron_variant	Intron 1 of 6	3		ENSP00000411309.1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117888 AN: 151936 Hom.: 45894 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.785

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 117992 AN: 152054 Hom.: 45942 Cov.: 31 AF XY: 0.777 AC XY: 57718 AN XY: 74316

African (AFR) AF: 0.744 AC: 30831 AN: 41464

American (AMR) AF: 0.840 AC: 12831 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2677 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5012 AN: 5178

South Asian (SAS) AF: 0.815 AC: 3925 AN: 4814

European-Finnish (FIN) AF: 0.739 AC: 7806 AN: 10564

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52287 AN: 67978

Other (OTH) AF: 0.787 AC: 1655 AN: 2102

Alfa AF: 0.775 Hom.: 187995

Bravo AF: 0.785

Asia WGS AF: 0.897 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.39
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2265932; hg19: chr1-179267783;