rs6670868

chr1-180340672-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ACBD6	NM_032360.4	c.664-25950A>G		intron_variant		ENST00000367595.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACBD6	ENST00000367595.4	c.664-25950A>G		intron_variant		1	NM_032360.4	P1

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

Gnomad4 AFR AF: 0.0392

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0115

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.0589

Alfa AF: 0.0556 Hom.: 126

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

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: rs6670868; hg19: chr1-180309807;