rs2862616

Variant names:

• chr1-179326397-A-G
• rs2862616
• NM_003101.6:c.177+2902A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003101.6(SOAT1):​c.177+2902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,988 control chromosomes in the GnomAD database, including 19,707 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 0.50 (19707 hom., cov: 31)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 4 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 = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.177+2902A>G		intron_variant	Intron 3 of 15	ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.177+2902A>G		intron_variant	Intron 3 of 15	1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.4-9109A>G		intron_variant	Intron 2 of 14	1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.-19+2902A>G		intron_variant	Intron 2 of 14	2		ENSP00000441356.1
SOAT1	ENST00000426956.1	c.177+2902A>G		intron_variant	Intron 3 of 6	3		ENSP00000411309.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75431 AN: 151870 Hom.: 19682 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.497 AC: 75496 AN: 151988 Hom.: 19707 Cov.: 31 AF XY: 0.500 AC XY: 37167 AN XY: 74280

African (AFR) AF: 0.362 AC: 15001 AN: 41418

American (AMR) AF: 0.640 AC: 9785 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3466

East Asian (EAS) AF: 0.845 AC: 4377 AN: 5182

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4958 AN: 10532

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35247 AN: 67974

Other (OTH) AF: 0.519 AC: 1098 AN: 2114

Alfa AF: 0.525 Hom.: 6382

Bravo AF: 0.508

Asia WGS AF: 0.728 AC: 2531 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	6.4
DANN	Benign	0.39
PhyloP100		-0.93
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: rs2862616; hg19: chr1-179295532;