1-54604313-T-C

Variant names:

• chr1-54604313-T-C
• rs746503
• NM_147161.4:c.1153-33T>C

Variant summary

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

The NM_147161.4(ACOT11):​c.1153-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 1,596,046 control chromosomes in the GnomAD database, including 288,350 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 0.58 (25428 hom., cov: 30)
  • Exomes 𝑓: 0.60 (262922 hom.)
• Consequence: ACOT11 NM_147161.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 15 publications found

Genes affected

ACOT11 (HGNC:18156): (acyl-CoA thioesterase 11) This gene encodes a member of the acyl-CoA thioesterase family which catalyse the conversion of activated fatty acids to the corresponding non-esterified fatty acid and coenzyme A. Expression of a mouse homolog in brown adipose tissue is induced by low temperatures and repressed by warm temperatures. Higher levels of expression of the mouse homolog has been found in obesity-resistant mice compared with obesity-prone mice, suggesting a role of acyl-CoA thioesterase 11 in obesity. Alternative splicing results in transcript variants. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACOT11	NM_147161.4	c.1153-33T>C		intron_variant	Intron 11 of 15	ENST00000343744.7	NP_671517.1
ACOT11	NM_015547.4	c.1153-33T>C		intron_variant	Intron 11 of 16		NP_056362.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACOT11	ENST00000343744.7	c.1153-33T>C		intron_variant	Intron 11 of 15	1	NM_147161.4	ENSP00000340260.2
ACOT11	ENST00000371316.3	c.1153-33T>C		intron_variant	Intron 11 of 16	1		ENSP00000360366.3
ACOT11	ENST00000481208.5	n.1231-33T>C		intron_variant	Intron 10 of 14	2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87175 AN: 151514 Hom.: 25413 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.593

GnomAD2 exomes AF: 0.572 AC: 142874 AN: 249564 AF XY: 0.577

Gnomad AFR exome AF: 0.510

Gnomad AMR exome AF: 0.514

Gnomad ASJ exome AF: 0.615

Gnomad EAS exome AF: 0.423

Gnomad FIN exome AF: 0.606

Gnomad NFE exome AF: 0.630

Gnomad OTH exome AF: 0.592

GnomAD4 exome AF: 0.601 AC: 868328 AN: 1444414 Hom.: 262922 Cov.: 27 AF XY: 0.600 AC XY: 431633 AN XY: 719422

African (AFR) AF: 0.499 AC: 16541 AN: 33136

American (AMR) AF: 0.517 AC: 23079 AN: 44606

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 16166 AN: 25996

East Asian (EAS) AF: 0.389 AC: 15371 AN: 39536

South Asian (SAS) AF: 0.511 AC: 43867 AN: 85818

European-Finnish (FIN) AF: 0.603 AC: 31769 AN: 52688

Middle Eastern (MID) AF: 0.612 AC: 3088 AN: 5046

European-Non Finnish (NFE) AF: 0.622 AC: 682995 AN: 1097862

Other (OTH) AF: 0.594 AC: 35452 AN: 59726

GnomAD4 genome AF: 0.575 AC: 87229 AN: 151632 Hom.: 25428 Cov.: 30 AF XY: 0.570 AC XY: 42240 AN XY: 74058

African (AFR) AF: 0.509 AC: 21033 AN: 41294

American (AMR) AF: 0.568 AC: 8661 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2182 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2152 AN: 5106

South Asian (SAS) AF: 0.481 AC: 2306 AN: 4794

European-Finnish (FIN) AF: 0.601 AC: 6316 AN: 10516

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.627 AC: 42571 AN: 67898

Other (OTH) AF: 0.595 AC: 1253 AN: 2106

Alfa AF: 0.612 Hom.: 51791

Bravo AF: 0.569

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.30
PhyloP100		-1.5
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: rs746503; hg19: chr1-55069986; COSMIC: COSV56363872; COSMIC: COSV56363872;