rs10561331

Variant names:

• chr11-108121200-CAAAAAA-C
• rs10561331
• NM_001386681.1:c.-199+4310_-199+4315delAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr11-108121200-CAAAAAA-C
• chr11-108121200-CAAAAAA-CA
• chr11-108121200-CAAAAAA-CAA
• chr11-108121200-CAAAAAA-CAAA
• chr11-108121200-CAAAAAA-CAAAA
• chr11-108121200-CAAAAAA-CAAAAA
• chr11-108121200-CAAAAAA-CAAAAAAA
• chr11-108121200-CAAAAAA-CAAAAAAAA
• chr11-108121200-CAAAAAA-CAAAAAAAAA
• chr11-108121200-CAAAAAA-CAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001386681.1(ACAT1):​c.-199+4310_-199+4315delAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 252,142 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000073 (0 hom.)
• Consequence: ACAT1 NM_001386681.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

Genes affected

ACAT1 (HGNC:93): (acetyl-CoA acetyltransferase 1) This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA. Defects in this gene are associated with 3-ketothiolase deficiency, an inborn error of isoleucine catabolism characterized by urinary excretion of 2-methyl-3-hydroxybutyric acid, 2-methylacetoacetic acid, tiglylglycine, and butanone. [provided by RefSeq, Feb 2009]

ENSG00000255467 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACAT1	NM_001386681.1	c.-199+4310_-199+4315delAAAAAA		intron_variant	Intron 1 of 11		NP_001373610.1
ACAT1	NM_001386682.1	c.-416+4310_-416+4315delAAAAAA		intron_variant	Intron 1 of 12		NP_001373611.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACAT1	ENST00000672284.1	c.-199+4299_-199+4304delAAAAAA		intron_variant	Intron 1 of 11			ENSP00000500444.1
ENSG00000255467	ENST00000525548.1	n.389+90_389+95delTTTTTT		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0000141 AC: 2 AN: 142076 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000140

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000727 AC: 8 AN: 109998 Hom.: 0 AF XY: 0.0000679 AC XY: 4 AN XY: 58930

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000264

Gnomad4 SAS exome AF: 0.000192

Gnomad4 FIN exome AF: 0.000157

Gnomad4 NFE exome AF: 0.0000311

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000141 AC: 2 AN: 142144 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 68714

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000140

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10561331; hg19: chr11-107991927;