chr10-15087403-T-C

Variant names:

• chr10-15087403-T-C
• rs11259474
• NM_001039844.3:c.12+1314A>G

Variant summary

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

The NM_001039844.3(ACBD7):​c.12+1314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,146 control chromosomes in the GnomAD database, including 6,794 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 0.24 (6794 hom., cov: 33)
• Consequence: ACBD7 NM_001039844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 7 publications found

Genes affected

ACBD7 (HGNC:17715): (acyl-CoA binding domain containing 7) Predicted to enable fatty-acyl-CoA binding activity and lipid binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACBD7-DCLRE1CP1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039844.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACBD7	NM_001039844.3	MANE Select	c.12+1314A>G		intron	N/A	NP_001034933.1
	ACBD7-DCLRE1CP1	NR_144471.1		n.60+1314A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACBD7	ENST00000356189.6	TSL:2 MANE Select	c.12+1314A>G		intron	N/A	ENSP00000367453.4
	ACBD7	ENST00000496890.1	TSL:3	n.176+903A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36252 AN: 152028 Hom.: 6772 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.239 AC: 36322 AN: 152146 Hom.: 6794 Cov.: 33 AF XY: 0.239 AC XY: 17776 AN XY: 74388

African (AFR) AF: 0.521 AC: 21609 AN: 41492

American (AMR) AF: 0.146 AC: 2227 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0877 AC: 304 AN: 3466

East Asian (EAS) AF: 0.317 AC: 1636 AN: 5162

South Asian (SAS) AF: 0.0910 AC: 439 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1815 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7694 AN: 68006

Other (OTH) AF: 0.207 AC: 438 AN: 2114

Alfa AF: 0.174 Hom.: 7431

Bravo AF: 0.253

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.49
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism (auto)

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: rs11259474; hg19: chr10-15129402;