1-180281025-T-C

Position:

• chr1-180281025-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047432084.1(ACBD6):​c.*586A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,056 control chromosomes in the GnomAD database, including 20,538 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 0.49 (20538 hom., cov: 32)
• Consequence: ACBD6 XM_047432084.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACBD6	XM_047432084.1	c.*586A>G		3_prime_UTR_variant	10/10		XP_047288040.1
ACBD6	XM_047432080.1	c.*174+281A>G		intron_variant			XP_047288036.1
ACBD6	XM_047432081.1	c.*301+281A>G		intron_variant			XP_047288037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACBD6	ENST00000642319.1	c.*174+281A>G		intron_variant				ENSP00000495710.1
ACBD6	ENST00000496993.5	n.639+281A>G		intron_variant		5
ACBD6	ENST00000645415.1	n.*407+281A>G		intron_variant				ENSP00000494507.1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73908 AN: 151938 Hom.: 20538 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.486 AC: 73898 AN: 152056 Hom.: 20538 Cov.: 32 AF XY: 0.491 AC XY: 36525 AN XY: 74314

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.489

Alfa AF: 0.578 Hom.: 13084

Bravo AF: 0.462

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs716760; hg19: chr1-180250160; COSMIC: COSV55374134; COSMIC: COSV55374134;