Menu
GeneBe

15-78173669-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_015162.5(ACSBG1):c.2013C>T(p.Asn671=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,614,194 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0073 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00081 ( 18 hom. )

Consequence

ACSBG1
NM_015162.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.54
Variant links:
Genes affected
ACSBG1 (HGNC:29567): (acyl-CoA synthetase bubblegum family member 1) The protein encoded by this gene possesses long-chain acyl-CoA synthetase activity. It is thought to play a central role in brain very long-chain fatty acids metabolism and myelinogenesis. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 15-78173669-G-A is Benign according to our data. Variant chr15-78173669-G-A is described in ClinVar as [Benign]. Clinvar id is 785502.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-4.54 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00726 (1106/152308) while in subpopulation AFR AF= 0.0256 (1064/41568). AF 95% confidence interval is 0.0243. There are 15 homozygotes in gnomad4. There are 520 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 15 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ACSBG1NM_015162.5 linkuse as main transcriptc.2013C>T p.Asn671= synonymous_variant 13/14 ENST00000258873.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACSBG1ENST00000258873.9 linkuse as main transcriptc.2013C>T p.Asn671= synonymous_variant 13/141 NM_015162.5 P1
ACSBG1ENST00000560817.5 linkuse as main transcriptc.1287C>T p.Asn429= synonymous_variant 9/105
ACSBG1ENST00000560183.1 linkuse as main transcriptn.599C>T non_coding_transcript_exon_variant 2/22
ACSBG1ENST00000560124.5 linkuse as main transcriptc.*1325C>T 3_prime_UTR_variant, NMD_transcript_variant 9/102

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00726
AC:
1105
AN:
152190
Hom.:
15
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0256
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00188
AC:
472
AN:
251486
Hom.:
7
AF XY:
0.00152
AC XY:
206
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.0255
Gnomad AMR exome
AF:
0.00107
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000105
Gnomad OTH exome
AF:
0.000814
GnomAD4 exome
AF:
0.000810
AC:
1184
AN:
1461886
Hom.:
18
Cov.:
31
AF XY:
0.000704
AC XY:
512
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.0282
Gnomad4 AMR exome
AF:
0.00125
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000629
Gnomad4 OTH exome
AF:
0.00161
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00726
AC:
1106
AN:
152308
Hom.:
15
Cov.:
32
AF XY:
0.00698
AC XY:
520
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0256
Gnomad4 AMR
AF:
0.00176
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00358
Hom.:
1
Bravo
AF:
0.00835
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.000436
EpiControl
AF:
0.000178

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 testingInvitaeMay 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.086
Dann
Benign
0.88

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: rs138480953; hg19: chr15-78466011; API