6-159775264-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_005891.3(ACAT2):ā€‹c.585T>Gā€‹(p.Ala195=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,614,202 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Genomes: š‘“ 0.0054 ( 9 hom., cov: 33)
Exomes š‘“: 0.00055 ( 7 hom. )

Consequence

ACAT2
NM_005891.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.11
Variant links:
Genes affected
ACAT2 (HGNC:94): (acetyl-CoA acetyltransferase 2) The product of this gene is an enzyme involved in lipid metabolism, and it encodes cytosolic acetoacetyl-CoA thiolase. This gene shows complementary overlapping with the 3-prime region of the TCP1 gene in both mouse and human. These genes are encoded on opposite strands of DNA, as well as in opposite transcriptional orientation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 6-159775264-T-G is Benign according to our data. Variant chr6-159775264-T-G is described in ClinVar as [Benign]. Clinvar id is 781017.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.11 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00542 (825/152340) while in subpopulation AFR AF= 0.0192 (797/41582). AF 95% confidence interval is 0.0181. There are 9 homozygotes in gnomad4. There are 420 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ACAT2NM_005891.3 linkuse as main transcriptc.585T>G p.Ala195= synonymous_variant 5/9 ENST00000367048.5
ACAT2NM_001303253.1 linkuse as main transcriptc.672T>G p.Ala224= synonymous_variant 5/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACAT2ENST00000367048.5 linkuse as main transcriptc.585T>G p.Ala195= synonymous_variant 5/91 NM_005891.3 P1Q9BWD1-1
ACAT2ENST00000467951.1 linkuse as main transcriptn.813T>G non_coding_transcript_exon_variant 5/53
ACAT2ENST00000472052.1 linkuse as main transcript upstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00543
AC:
826
AN:
152222
Hom.:
10
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0192
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00431
GnomAD3 exomes
AF:
0.00150
AC:
376
AN:
251410
Hom.:
4
AF XY:
0.00118
AC XY:
160
AN XY:
135878
show subpopulations
Gnomad AFR exome
AF:
0.0199
Gnomad AMR exome
AF:
0.00124
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000440
Gnomad OTH exome
AF:
0.000815
GnomAD4 exome
AF:
0.000553
AC:
808
AN:
1461862
Hom.:
7
Cov.:
30
AF XY:
0.000484
AC XY:
352
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.0187
Gnomad4 AMR exome
AF:
0.00143
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000234
Gnomad4 OTH exome
AF:
0.00139
GnomAD4 genome
AF:
0.00542
AC:
825
AN:
152340
Hom.:
9
Cov.:
33
AF XY:
0.00564
AC XY:
420
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0192
Gnomad4 AMR
AF:
0.000981
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00427
Alfa
AF:
0.00246
Hom.:
3
Bravo
AF:
0.00611
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
CADD
Benign
2.0
DANN
Benign
0.79

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41292466; hg19: chr6-160196296; API