rs11259474

Positions:

• chr10-15087403-T-C
• chr10-15087403-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACBD7	NM_001039844.3	c.12+1314A>G		intron_variant		ENST00000356189.6
ACBD7-DCLRE1CP1	NR_144471.1	n.60+1314A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACBD7	ENST00000356189.6	c.12+1314A>G		intron_variant		2	NM_001039844.3	P1
ACBD7	ENST00000496890.1	n.176+903A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.207

Alfa AF: 0.173 Hom.: 1603

Bravo AF: 0.253

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.49

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: rs11259474; hg19: chr10-15129402;