rs4421551

Variant names:

• chr1-179346763-C-A
• rs4421551
• NM_003101.6:c.1118-837C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.9).
• 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 rank	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.1118-837C>A		intron_variant	Intron 11 of 15	ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.1118-837C>A		intron_variant	Intron 11 of 15	1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.944-837C>A		intron_variant	Intron 10 of 14	1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.923-837C>A		intron_variant	Intron 10 of 14	2		ENSP00000441356.1

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

African (AFR) AF: 0.872 AC: 36188 AN: 41484

American (AMR) AF: 0.894 AC: 13647 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2647 AN: 3464

East Asian (EAS) AF: 0.908 AC: 4687 AN: 5164

South Asian (SAS) AF: 0.825 AC: 3971 AN: 4814

European-Finnish (FIN) AF: 0.914 AC: 9679 AN: 10588

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59850 AN: 68004

Other (OTH) AF: 0.848 AC: 1792 AN: 2114

Alfa AF: 0.880 Hom.: 7644

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
PhyloP100		-0.63
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: rs4421551; hg19: chr1-179315898;