rs1044925

chr1-179354603-C-Achr1-179354603-C-Gchr1-179354603-C-T

Variant summary

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

The NM_003101.6(SOAT1):c.*962C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,922 control chromosomes in the GnomAD database, including 34,090 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 0.67 (34090 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SOAT1 NM_003101.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOAT1	NM_003101.6	c.*962C>A		3_prime_UTR_variant	16/16	ENST00000367619.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOAT1	ENST00000367619.8	c.*962C>A		3_prime_UTR_variant	16/16	1	NM_003101.6	P1
SOAT1	ENST00000540564.5	c.*962C>A		3_prime_UTR_variant	15/15	1
SOAT1	ENST00000539888.5	c.*962C>A		3_prime_UTR_variant	15/15	2

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101416 AN: 151804 Hom.: 34054 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.648

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.668 AC: 101505 AN: 151922 Hom.: 34090 Cov.: 32 AF XY: 0.668 AC XY: 49570 AN XY: 74252

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.648

Alfa AF: 0.606 Hom.: 3228

Bravo AF: 0.676

Asia WGS AF: 0.775 AC: 2676 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.6
Dann	Benign	0.54

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: rs1044925; hg19: chr1-179323738;