rs2152319

Positions:

• chr1-179346222-C-A
• chr1-179346222-C-G

Variant summary

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

The NM_003101.6(SOAT1):​c.1117+1146C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,950 control chromosomes in the GnomAD database, including 24,276 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 0.56 (24276 hom., cov: 32)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

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 = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOAT1	NM_003101.6	c.1117+1146C>A		intron_variant		ENST00000367619.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOAT1	ENST00000367619.8	c.1117+1146C>A		intron_variant		1	NM_003101.6	P1
SOAT1	ENST00000540564.5	c.943+1146C>A		intron_variant		1
SOAT1	ENST00000539888.5	c.922+1146C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84841 AN: 151830 Hom.: 24266 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.559 AC: 84901 AN: 151950 Hom.: 24276 Cov.: 32 AF XY: 0.562 AC XY: 41740 AN XY: 74268

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.561

Alfa AF: 0.574 Hom.: 32681

Bravo AF: 0.559

Asia WGS AF: 0.748 AC: 2602 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	0.096
DANN	Benign	0.66

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: rs2152319; hg19: chr1-179315357;