rs10494526

Variant names:

• chr1-180310575-G-A
• rs10494526
• NM_032360.4:c.694+4117C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-180310575-G-A
• chr1-180310575-G-C

Variant summary

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

The NM_032360.4(ACBD6):​c.694+4117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 152,250 control chromosomes in the GnomAD database, including 364 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 0.025 (364 hom., cov: 32)
• Consequence: ACBD6 NM_032360.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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.694+4117C>T		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.694+4117C>T		intron	N/A	ENSP00000356567.3	Q9BR61
	ACBD6	ENST00000937021.1		c.808+4117C>T		intron	N/A	ENSP00000607080.1
	ACBD6	ENST00000880422.1		c.763+4117C>T		intron	N/A	ENSP00000550481.1

Frequencies

GnomAD3 genomes AF: 0.0251 AC: 3814 AN: 152132 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.00490

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00542

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0250 AC: 3813 AN: 152250 Hom.: 364 Cov.: 32 AF XY: 0.0283 AC XY: 2103 AN XY: 74432

African (AFR) AF: 0.00488 AC: 203 AN: 41556

American (AMR) AF: 0.0847 AC: 1296 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1539 AN: 5172

South Asian (SAS) AF: 0.0511 AC: 246 AN: 4818

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00543 AC: 369 AN: 68016

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.0113 Hom.: 22

Bravo AF: 0.0301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.51
DANN	Benign	0.53
PhyloP100		-0.18

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: rs10494526; hg19: chr1-180279710;