chr1-179326397-A-G

Position:

• chr1-179326397-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

SOAT1 (HGNC:):

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 = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.177+2902A>G		intron_variant		ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.177+2902A>G		intron_variant		1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.4-9109A>G		intron_variant		1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.-19+2902A>G		intron_variant		2		ENSP00000441356.1
SOAT1	ENST00000426956.1	c.177+2902A>G		intron_variant		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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.519

Alfa AF: 0.503 Hom.: 2462

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

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: rs2862616; hg19: chr1-179295532;