rs1094597

Variant names:

• chr1-180325632-T-C
• rs1094597
• NM_032360.4:c.664-10910A>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.664-10910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,228 control chromosomes in the GnomAD database, including 226 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 0.045 (226 hom., cov: 32)
• Consequence: ACBD6 NM_032360.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032360.4. 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
	ACBD6	NM_032360.4	MANE Select	c.664-10910A>G		intron	N/A	NP_115736.1	Q9BR61

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACBD6	ENST00000367595.4	TSL:1 MANE Select	c.664-10910A>G		intron	N/A	ENSP00000356567.3	Q9BR61
	ACBD6	ENST00000937021.1		c.778-10910A>G		intron	N/A	ENSP00000607080.1
	ACBD6	ENST00000880422.1		c.733-10910A>G		intron	N/A	ENSP00000550481.1

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6881 AN: 152110 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0452 AC: 6886 AN: 152228 Hom.: 226 Cov.: 32 AF XY: 0.0464 AC XY: 3451 AN XY: 74420

African (AFR) AF: 0.0114 AC: 475 AN: 41568

American (AMR) AF: 0.0375 AC: 573 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 208 AN: 3464

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5176

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10574

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4028 AN: 68022

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

Alfa AF: 0.0513 Hom.: 31

Bravo AF: 0.0382

Asia WGS AF: 0.0490 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.19
PhyloP100		-1.0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1094597;

hg19: chr1-180294767;