1-179300309-T-C

Position:

• chr1-179300309-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SOAT1	NM_003101.6	c.-8-2368T>C		intron_variant		ENST00000367619.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOAT1	ENST00000367619.8	c.-8-2368T>C		intron_variant		1	NM_003101.6	P1
SOAT1	ENST00000540564.5	c.-123-2368T>C		intron_variant		1
SOAT1	ENST00000426956.1	c.-8-2368T>C		intron_variant		3
SOAT1	ENST00000539888.5	c.-78+6373T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.789

Alfa AF: 0.773 Hom.: 5653

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2247071; hg19: chr1-179269444;