NM_001318890.3:c.1299+417A>G

Variant names:

• chr16-20636322-T-C
• rs234993
• NM_001318890.3:c.1299+417A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318890.3(ACSM1):​c.1299+417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 152,238 control chromosomes in the GnomAD database, including 631 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 0.080 (631 hom., cov: 31)
• Consequence: ACSM1 NM_001318890.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 10 publications found

Genes affected

ACSM1 (HGNC:18049): (acyl-CoA synthetase medium chain family member 1) Enables CoA-ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACSM3 (HGNC:10522): (acyl-CoA synthetase medium chain family member 3) Enables butyrate-CoA ligase activity. Predicted to be involved in acyl-CoA metabolic process and fatty acid biosynthetic process. Located in mitochondrion. Implicated in IgA glomerulonephritis. Biomarker of ulcerative colitis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318890.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSM1	NM_001318890.3	MANE Select	c.1299+417A>G		intron	N/A	NP_001305819.1	Q08AH1-1
	ACSM1	NM_052956.3		c.1299+417A>G		intron	N/A	NP_443188.2	Q08AH1-1
	ACSM1	NR_134918.2		n.1202+1049A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSM1	ENST00000520010.6	TSL:1 MANE Select	c.1299+417A>G		intron	N/A	ENSP00000428047.1	Q08AH1-1
	ACSM1	ENST00000307493.8	TSL:1	c.1299+417A>G		intron	N/A	ENSP00000301956.3	Q08AH1-1
	ACSM1	ENST00000519745.5	TSL:1	n.*519+1049A>G		intron	N/A	ENSP00000428650.1	Q08AH1-2

Frequencies

GnomAD3 genomes AF: 0.0799 AC: 12155 AN: 152120 Hom.: 630 Cov.: 31

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0798 AC: 12152 AN: 152238 Hom.: 631 Cov.: 31 AF XY: 0.0804 AC XY: 5981 AN XY: 74426

African (AFR) AF: 0.0347 AC: 1441 AN: 41540

American (AMR) AF: 0.0572 AC: 875 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5174

South Asian (SAS) AF: 0.156 AC: 754 AN: 4824

European-Finnish (FIN) AF: 0.0995 AC: 1055 AN: 10600

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6229 AN: 68010

Other (OTH) AF: 0.0818 AC: 173 AN: 2116

Alfa AF: 0.0802 Hom.: 913

Bravo AF: 0.0724

Asia WGS AF: 0.151 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.75
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs234993; hg19: chr16-20647644;