Variant chr13-76955509-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001258406.2(ACOD1):c.455A>G(p.Asn152Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00828 in 1,550,634 control chromosomes in the GnomAD database, including 895 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.043 ( 493 hom., cov: 33)

Exomes 𝑓: 0.0045 ( 402 hom. )

Consequence

ACOD1
NM_001258406.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.270

Variant links:

Genes affected

ACOD1 (HGNC:33904): (aconitate decarboxylase 1) Enables aconitate decarboxylase activity. Involved in defense response; positive regulation of antimicrobial humoral response; and tolerance induction to lipopolysaccharide. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACOD1 links:

LOC105370269 (HGNC:):

LOC105370269 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014506578).

BP6

Variant 13-76955509-A-G is Benign according to our data. Variant chr13-76955509-A-G is described in ClinVar as [Benign]. Clinvar id is 776801.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ACOD1	NM_001258406.2 linkuse as main transcript	c.455A>G	p.Asn152Ser	missense_variant	4/5	ENST00000377462.6	NP_001245335.1
LOC105370269	XR_001749929.1 linkuse as main transcript	n.213-12638T>C		intron_variant, non_coding_transcript_variant
ACOD1	XM_047430581.1 linkuse as main transcript	c.359A>G	p.Asn120Ser	missense_variant	3/4		XP_047286537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACOD1	ENST00000377462.6 linkuse as main transcript	c.455A>G	p.Asn152Ser	missense_variant	4/5	5	NM_001258406.2	ENSP00000366682	P1

Frequencies

GnomAD3 genomes

AF:

0.0428

AC:

6514

AN:

152210

Hom.:

489

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0192

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000485

Gnomad OTH

AF:

0.0253

GnomAD3 exomes

AF:

0.00875

AC:

1307

AN:

149290

Hom.:

AF XY:

0.00700

AC XY:

562

AN XY:

80328

show subpopulations

Gnomad AFR exome

AF:

0.147

Gnomad AMR exome

AF:

0.00892

Gnomad ASJ exome

AF:

0.000239

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000488

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000780

Gnomad OTH exome

AF:

0.00740

GnomAD4 exome

AF:

0.00451

AC:

6305

AN:

1398306

Hom.:

402

Cov.:

AF XY:

0.00394

AC XY:

2714

AN XY:

689676

show subpopulations

Gnomad4 AFR exome

AF:

0.152

Gnomad4 AMR exome

AF:

0.00972

Gnomad4 ASJ exome

AF:

0.000119

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000480

Gnomad4 FIN exome

AF:

0.0000415

Gnomad4 NFE exome

AF:

0.000413

Gnomad4 OTH exome

AF:

0.0100

GnomAD4 genome

AF:

0.0429

AC:

6538

AN:

152328

Hom.:

493

Cov.:

AF XY:

0.0417

AC XY:

3108

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.0191

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.0251

Alfa

AF:

0.0274

Hom.:

137

Bravo

AF:

0.0481

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ExAC

AF:

0.00820

AC:

175

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 21, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.0

DANN

Benign

0.50

DEOGEN2

Benign

0.0034

T;.

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.088

LIST_S2

Benign

0.82

T;T

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.55

N;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.19

PROVEAN

Benign

0.19

N;N

REVEL

Benign

0.018

Sift

Benign

0.50

T;T

Sift4G

Benign

0.78

T;T

Vest4

0.059

MVP

0.048

ClinPred

0.0032

GERP RS

0.18

Varity_R

0.053

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over