rs4986172

Positions:

• chr17-45138914-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACBD4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACBD4	NM_001135705.3	c.650-107C>T		intron_variant		ENST00000321854.13	NP_001129177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACBD4	ENST00000321854.13	c.650-107C>T		intron_variant		1	NM_001135705.3	ENSP00000314440.8
ACBD4	ENST00000591859.5	c.688-107C>T		intron_variant		1		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

Gnomad4 AFR exome AF: 0.634

Gnomad4 AMR exome AF: 0.435

Gnomad4 ASJ exome AF: 0.381

Gnomad4 EAS exome AF: 0.436

Gnomad4 SAS exome AF: 0.362

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.385

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

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.408

Alfa AF: 0.367 Hom.: 19805

Bravo AF: 0.452

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.038
DANN	Benign	0.33

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: rs4986172; hg19: chr17-43216281;