rs3777664

Positions:

• chr6-24693618-G-A
• chr6-24693618-G-C

Variant summary

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

The NM_018473.4(ACOT13):​c.82-4265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,116 control chromosomes in the GnomAD database, including 42,912 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 0.75 (42912 hom., cov: 31)
• Consequence: ACOT13 NM_018473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

ACOT13 (HGNC:20999): (acyl-CoA thioesterase 13) This gene encodes a member of the thioesterase superfamily. In humans, the protein co-localizes with microtubules and is essential for sustained cell proliferation. The orthologous mouse protein forms a homotetramer and is associated with mitochondria. The mouse protein functions as a medium- and long-chain acyl-CoA thioesterase. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2009]

LOC124901278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACOT13	NM_018473.4	c.82-4265G>A		intron_variant		ENST00000230048.5	NP_060943.1
LOC124901278	XR_007059508.1	n.1556C>T		non_coding_transcript_exon_variant	2/2
ACOT13	NM_001160094.2	c.13-4265G>A		intron_variant			NP_001153566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOT13	ENST00000230048.5	c.82-4265G>A		intron_variant		1	NM_018473.4	ENSP00000230048	P1
ACOT13	ENST00000537591.5	c.13-4265G>A		intron_variant		1		ENSP00000445552
ACOT13	ENST00000476436.1	n.293-4265G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113698 AN: 151998 Hom.: 42866 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.748 AC: 113801 AN: 152116 Hom.: 42912 Cov.: 31 AF XY: 0.746 AC XY: 55498 AN XY: 74376

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.725

Alfa AF: 0.715 Hom.: 66380

Bravo AF: 0.763

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.76

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: rs3777664; hg19: chr6-24693846;