rs1044925

Variant names:

• chr1-179354603-C-A
• rs1044925
• NM_003101.6:c.*962C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-179354603-C-A
• chr1-179354603-C-G
• chr1-179354603-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 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=-0.8).
• 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 rank	MANE	Protein	UniProt
SOAT1	NM_003101.6	c.*962C>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000367619.8	NP_003092.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOAT1	ENST00000367619.8	c.*962C>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_003101.6	ENSP00000356591.3
SOAT1	ENST00000540564.5	c.*962C>A		3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000445315.1
SOAT1	ENST00000539888.5	c.*962C>A		3_prime_UTR_variant	Exon 15 of 15	2		ENSP00000441356.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.711 AC: 29482 AN: 41452

American (AMR) AF: 0.692 AC: 10549 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1829 AN: 3462

East Asian (EAS) AF: 0.878 AC: 4539 AN: 5170

South Asian (SAS) AF: 0.647 AC: 3116 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6445 AN: 10528

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43429 AN: 67936

Other (OTH) AF: 0.648 AC: 1364 AN: 2104

Alfa AF: 0.609 Hom.: 3403

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
PhyloP100		0.99
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: rs1044925; hg19: chr1-179323738;