chr16-20543937-T-A

Position:

• chr16-20543937-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001105069.2(ACSM2B):​c.1282-675A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,150 control chromosomes in the GnomAD database, including 1,505 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (1505 hom., cov: 32)
• Consequence: ACSM2B NM_001105069.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACSM2B	NM_001105069.2	c.1282-675A>T		intron_variant		ENST00000329697.10	NP_001098539.1
ACSM2B	NM_001410902.1	c.1045-675A>T		intron_variant			NP_001397831.1
ACSM2B	NM_182617.4	c.1282-675A>T		intron_variant			NP_872423.3
ACSM2B	XR_001751899.3	n.1562-675A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSM2B	ENST00000329697.10	c.1282-675A>T		intron_variant		1	NM_001105069.2	ENSP00000327453	P1

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 15184 AN: 152032 Hom.: 1495 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.0766

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.100 AC: 15250 AN: 152150 Hom.: 1505 Cov.: 32 AF XY: 0.101 AC XY: 7508 AN XY: 74394

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0258

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0688 Hom.: 121

Bravo AF: 0.110

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs7499271; hg19: chr16-20555259;