1-179300309-T-C

Variant names:

• chr1-179300309-T-C
• rs2247071
• NM_003101.6:c.-8-2368T>C

Variant summary

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

The NM_003101.6(SOAT1):​c.-8-2368T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,046 control chromosomes in the GnomAD database, including 46,180 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 (46180 hom., cov: 30)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.-8-2368T>C		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.-8-2368T>C		intron_variant	Intron 1 of 15	1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.-123-2368T>C		intron_variant	Intron 1 of 14	1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.-78+6373T>C		intron_variant	Intron 1 of 14	2		ENSP00000441356.1
SOAT1	ENST00000426956.1	c.-8-2368T>C		intron_variant	Intron 1 of 6	3		ENSP00000411309.1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118174 AN: 151928 Hom.: 46129 Cov.: 30

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.778 AC: 118281 AN: 152046 Hom.: 46180 Cov.: 30 AF XY: 0.778 AC XY: 57854 AN XY: 74318

African (AFR) AF: 0.751 AC: 31145 AN: 41464

American (AMR) AF: 0.841 AC: 12836 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2679 AN: 3468

East Asian (EAS) AF: 0.968 AC: 5008 AN: 5176

South Asian (SAS) AF: 0.813 AC: 3917 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7799 AN: 10562

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

European-Non Finnish (NFE) AF: 0.769 AC: 52264 AN: 67988

Other (OTH) AF: 0.789 AC: 1667 AN: 2112

Alfa AF: 0.772 Hom.: 5878

Bravo AF: 0.787

Asia WGS AF: 0.898 AC: 3120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		-0.13
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: rs2247071; hg19: chr1-179269444;