rs4421551

Positions:

• chr1-179346763-C-A

Variant summary

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

The NM_003101.6(SOAT1):​c.1118-837C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,106 control chromosomes in the GnomAD database, including 58,622 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 0.88 (58622 hom., cov: 31)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOAT1	NM_003101.6	c.1118-837C>A		intron_variant		ENST00000367619.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOAT1	ENST00000367619.8	c.1118-837C>A		intron_variant		1	NM_003101.6	P1
SOAT1	ENST00000540564.5	c.944-837C>A		intron_variant		1
SOAT1	ENST00000539888.5	c.923-837C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133340 AN: 151988 Hom.: 58568 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.877 AC: 133453 AN: 152106 Hom.: 58622 Cov.: 31 AF XY: 0.878 AC XY: 65255 AN XY: 74350

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.848

Alfa AF: 0.881 Hom.: 7366

Bravo AF: 0.876

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.72

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: rs4421551; hg19: chr1-179315898;