NM_003101.6:c.1117+1146C>A

Variant names:

• chr1-179346222-C-A
• rs2152319
• NM_003101.6:c.1117+1146C>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.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
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003101.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOAT1	NM_003101.6	MANE Select	c.1117+1146C>A		intron	N/A	NP_003092.4
	SOAT1	NM_001252511.2		c.943+1146C>A		intron	N/A	NP_001239440.1
	SOAT1	NM_001252512.2		c.922+1146C>A		intron	N/A	NP_001239441.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOAT1	ENST00000367619.8	TSL:1 MANE Select	c.1117+1146C>A		intron	N/A	ENSP00000356591.3
	SOAT1	ENST00000540564.5	TSL:1	c.943+1146C>A		intron	N/A	ENSP00000445315.1
	SOAT1	ENST00000539888.5	TSL:2	c.922+1146C>A		intron	N/A	ENSP00000441356.1

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

African (AFR) AF: 0.464 AC: 19229 AN: 41432

American (AMR) AF: 0.631 AC: 9618 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3468

East Asian (EAS) AF: 0.877 AC: 4531 AN: 5166

South Asian (SAS) AF: 0.620 AC: 2991 AN: 4822

European-Finnish (FIN) AF: 0.562 AC: 5928 AN: 10542

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39169 AN: 67954

Other (OTH) AF: 0.561 AC: 1183 AN: 2108

Alfa AF: 0.571 Hom.: 41291

Bravo AF: 0.559

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.096
DANN	Benign	0.66
PhyloP100		-2.5
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: rs2152319; hg19: chr1-179315357;