Variant chr16-20548432-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001105069.2(ACSM2B):c.936T>C(p.Pro312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00367 in 1,611,690 control chromosomes in the GnomAD database, including 156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 88 hom., cov: 32)

Exomes 𝑓: 0.0019 ( 68 hom. )

Consequence

ACSM2B
NM_001105069.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0760

Variant links:

Genes affected

ACSM2B (HGNC:30931): (acyl-CoA synthetase medium chain family member 2B) Enables benzoate-CoA ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACSM2B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 16-20548432-A-G is Benign according to our data. Variant chr16-20548432-A-G is described in ClinVar as [Benign]. Clinvar id is 786754.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.076 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACSM2B	NM_001105069.2 linkuse as main transcript	c.936T>C	p.Pro312=	synonymous_variant	7/14	ENST00000329697.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACSM2B	ENST00000329697.10 linkuse as main transcript	c.936T>C	p.Pro312=	synonymous_variant	7/14	1	NM_001105069.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0206

AC:

3128

AN:

151864

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0640

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00845

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0135

Gnomad FIN

AF:

0.0146

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00171

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00236

AC:

592

AN:

250382

Hom.:

AF XY:

0.00206

AC XY:

279

AN XY:

135322

show subpopulations

Gnomad AFR exome

AF:

0.0221

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.000198

Gnomad EAS exome

AF:

0.000653

Gnomad SAS exome

AF:

0.00362

Gnomad FIN exome

AF:

0.000840

Gnomad NFE exome

AF:

0.000282

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00191

AC:

2788

AN:

1459710

Hom.:

Cov.:

AF XY:

0.00205

AC XY:

1490

AN XY:

726102

show subpopulations

Gnomad4 AFR exome

AF:

0.0251

Gnomad4 AMR exome

AF:

0.00193

Gnomad4 ASJ exome

AF:

0.000498

Gnomad4 EAS exome

AF:

0.000605

Gnomad4 SAS exome

AF:

0.00817

Gnomad4 FIN exome

AF:

0.00976

Gnomad4 NFE exome

AF:

0.000364

Gnomad4 OTH exome

AF:

0.00335

GnomAD4 genome

AF:

0.0206

AC:

3134

AN:

151980

Hom.:

Cov.:

AF XY:

0.0210

AC XY:

1557

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.0639

Gnomad4 AMR

AF:

0.00844

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0137

Gnomad4 FIN

AF:

0.0146

Gnomad4 NFE

AF:

0.00171

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00149

Hom.:

Bravo

AF:

0.0217

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 17, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.7

DANN

Benign

0.58

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