rs10494526

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACBD6	NM_032360.4	c.694+4117C>T		intron_variant		ENST00000367595.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACBD6	ENST00000367595.4	c.694+4117C>T		intron_variant		1	NM_032360.4	P1

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

Gnomad4 AFR AF: 0.00488

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.0511

Gnomad4 FIN AF: 0.00330

Gnomad4 NFE AF: 0.00543

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0117 Hom.: 20

Bravo AF: 0.0301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs10494526; hg19: chr1-180279710;