NM_032360.4:c.664-25950A>G

Variant names:

• chr1-180340672-T-C
• rs6670868
• NM_032360.4:c.664-25950A>G

Variant summary

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

The NM_032360.4(ACBD6):​c.664-25950A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 151,372 control chromosomes in the GnomAD database, including 250 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 0.051 (250 hom., cov: 30)
• Consequence: ACBD6 NM_032360.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 3 publications found

Genes affected

ACBD6 (HGNC:23339): (acyl-CoA binding domain containing 6) Predicted to enable fatty-acyl-CoA binding activity and lipid binding activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACBD6 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with progressive movement abnormalities

  Inheritance: AR Classification: STRONG Submitted by: G2P
• intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACBD6	NM_032360.4	c.664-25950A>G		intron_variant	Intron 6 of 7	ENST00000367595.4	NP_115736.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACBD6	ENST00000367595.4	c.664-25950A>G		intron_variant	Intron 6 of 7	1	NM_032360.4	ENSP00000356567.3

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7669 AN: 151254 Hom.: 246 Cov.: 30

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0524

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

GnomAD4 genome AF: 0.0508 AC: 7690 AN: 151372 Hom.: 250 Cov.: 30 AF XY: 0.0509 AC XY: 3761 AN XY: 73958

African (AFR) AF: 0.0392 AC: 1621 AN: 41304

American (AMR) AF: 0.0566 AC: 859 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 166 AN: 3452

East Asian (EAS) AF: 0.0115 AC: 59 AN: 5146

South Asian (SAS) AF: 0.0894 AC: 428 AN: 4790

European-Finnish (FIN) AF: 0.0493 AC: 516 AN: 10456

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3817 AN: 67752

Other (OTH) AF: 0.0589 AC: 124 AN: 2104

Alfa AF: 0.0557 Hom.: 178

Bravo AF: 0.0492

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.87
PhyloP100		-0.071

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: rs6670868; hg19: chr1-180309807;