chr17-45138914-C-T

Variant names:

• chr17-45138914-C-T
• rs4986172
• NM_001135705.3:c.650-107C>T

Variant summary

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

The NM_001135705.3(ACBD4):​c.650-107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,208,418 control chromosomes in the GnomAD database, including 86,657 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 0.44 (15766 hom., cov: 32)
  • Exomes 𝑓: 0.36 (70891 hom.)
• Consequence: ACBD4 NM_001135705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 63 publications found

Genes affected

ACBD4 (HGNC:23337): (acyl-CoA binding domain containing 4) This gene encodes a member of the acyl-coenzyme A binding domain containing protein family. All family members contain the conserved acyl-Coenzyme A binding domain, which binds acyl-CoA thiol esters. They are thought to play roles in acyl-CoA dependent lipid metabolism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135705.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACBD4	NM_001135705.3	MANE Select	c.650-107C>T		intron	N/A	NP_001129177.1
	ACBD4	NM_001135706.3		c.688-107C>T		intron	N/A	NP_001129178.1
	ACBD4	NM_001321352.2		c.688-107C>T		intron	N/A	NP_001308281.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACBD4	ENST00000321854.13	TSL:1 MANE Select	c.650-107C>T		intron	N/A	ENSP00000314440.8
	ACBD4	ENST00000586346.5	TSL:1	c.688-107C>T		intron	N/A	ENSP00000465484.1
	ACBD4	ENST00000591859.5	TSL:1	c.688-107C>T		intron	N/A	ENSP00000465610.1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66563 AN: 151980 Hom.: 15746 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.409

GnomAD4 exome AF: 0.361 AC: 381328 AN: 1056320 Hom.: 70891 AF XY: 0.360 AC XY: 191476 AN XY: 531994

African (AFR) AF: 0.634 AC: 16121 AN: 25414

American (AMR) AF: 0.435 AC: 14530 AN: 33406

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 8150 AN: 21390

East Asian (EAS) AF: 0.436 AC: 15106 AN: 34616

South Asian (SAS) AF: 0.362 AC: 25440 AN: 70360

European-Finnish (FIN) AF: 0.375 AC: 13238 AN: 35322

Middle Eastern (MID) AF: 0.408 AC: 1382 AN: 3390

European-Non Finnish (NFE) AF: 0.343 AC: 269480 AN: 785946

Other (OTH) AF: 0.385 AC: 17881 AN: 46476

GnomAD4 genome AF: 0.438 AC: 66629 AN: 152098 Hom.: 15766 Cov.: 32 AF XY: 0.441 AC XY: 32782 AN XY: 74370

African (AFR) AF: 0.617 AC: 25587 AN: 41488

American (AMR) AF: 0.439 AC: 6712 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3466

East Asian (EAS) AF: 0.454 AC: 2344 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1828 AN: 4826

European-Finnish (FIN) AF: 0.403 AC: 4260 AN: 10582

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23269 AN: 67960

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.378 Hom.: 48101

Bravo AF: 0.452

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.038
DANN	Benign	0.33
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4986172; hg19: chr17-43216281;