rs2493121

Positions:

• chr1-179302981-T-A
• chr1-179302981-T-C
• chr1-179302981-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003101.6(SOAT1):​c.118+179T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,956 control chromosomes in the GnomAD database, including 30,180 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 0.62 (30180 hom., cov: 31)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.118+179T>A		intron_variant		ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.118+179T>A		intron_variant		1	NM_003101.6	ENSP00000356591	P1
SOAT1	ENST00000540564.5	c.3+179T>A		intron_variant		1		ENSP00000445315
SOAT1	ENST00000426956.1	c.118+179T>A		intron_variant		3		ENSP00000411309
SOAT1	ENST00000539888.5	c.-78+9045T>A		intron_variant		2		ENSP00000441356

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94252 AN: 151836 Hom.: 30154 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.621 AC: 94329 AN: 151956 Hom.: 30180 Cov.: 31 AF XY: 0.624 AC XY: 46323 AN XY: 74272

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.659

Alfa AF: 0.630 Hom.: 3804

Bravo AF: 0.628

Asia WGS AF: 0.818 AC: 2842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.42

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: rs2493121; hg19: chr1-179272116;