rs7118396

Variant names:

• chr11-47248385-C-T
• rs7118396
• NM_001610.4:c.115-252G>A

Variant summary

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

The NM_001610.4(ACP2):​c.115-252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,472,246 control chromosomes in the GnomAD database, including 35,675 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 0.26 (6317 hom., cov: 32)
  • Exomes 𝑓: 0.19 (29358 hom.)
• Consequence: ACP2 NM_001610.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 21 publications found

Genes affected

ACP2 (HGNC:123): (acid phosphatase 2, lysosomal) The protein encoded by this gene belongs to the histidine acid phosphatase family, which hydrolyze orthophosphoric monoesters to alcohol and phosphate. This protein is localized to the lysosomal membrane, and is chemically and genetically distinct from the red cell acid phosphatase. Mice lacking this gene showed multiple defects, including bone structure alterations, lysosomal storage defects, and an increased tendency towards seizures. An enzymatically-inactive allele of this gene in mice showed severe growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2017]

NR1H3 (HGNC:7966): (nuclear receptor subfamily 1 group H member 3) The protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily. The NR1 family members are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and intestine. It forms a heterodimer with retinoid X receptor (RXR), and regulates expression of target genes containing retinoid response elements. Studies in mice lacking this gene suggest that it may play an important role in the regulation of cholesterol homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001610.4. 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
	ACP2	NM_001610.4	MANE Select	c.115-252G>A		intron	N/A	NP_001601.1
	NR1H3	NM_001251934.2		c.-125+30C>T		intron	N/A	NP_001238863.1
	NR1H3	NM_001251935.2		c.-166+30C>T		intron	N/A	NP_001238864.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACP2	ENST00000672073.1	MANE Select	c.115-252G>A		intron	N/A	ENSP00000500291.1
	NR1H3	ENST00000616973.4	TSL:1	c.-166+30C>T		intron	N/A	ENSP00000477707.1
	ACP2	ENST00000256997.9	TSL:1	c.115-252G>A		intron	N/A	ENSP00000256997.3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39225 AN: 151946 Hom.: 6315 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.186 AC: 244965 AN: 1320182 Hom.: 29358 Cov.: 22 AF XY: 0.186 AC XY: 121224 AN XY: 652456

African (AFR) AF: 0.380 AC: 11479 AN: 30178

American (AMR) AF: 0.357 AC: 12393 AN: 34708

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 3111 AN: 24066

East Asian (EAS) AF: 0.654 AC: 23040 AN: 35220

South Asian (SAS) AF: 0.235 AC: 18082 AN: 76926

European-Finnish (FIN) AF: 0.257 AC: 8896 AN: 34602

Middle Eastern (MID) AF: 0.162 AC: 897 AN: 5552

European-Non Finnish (NFE) AF: 0.153 AC: 156071 AN: 1023404

Other (OTH) AF: 0.198 AC: 10996 AN: 55526

GnomAD4 genome AF: 0.258 AC: 39239 AN: 152064 Hom.: 6317 Cov.: 32 AF XY: 0.268 AC XY: 19903 AN XY: 74352

African (AFR) AF: 0.381 AC: 15818 AN: 41484

American (AMR) AF: 0.272 AC: 4153 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3360 AN: 5166

South Asian (SAS) AF: 0.236 AC: 1139 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3115 AN: 10556

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10639 AN: 67978

Other (OTH) AF: 0.211 AC: 444 AN: 2106

Alfa AF: 0.256 Hom.: 1712

Bravo AF: 0.265

Asia WGS AF: 0.342 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.8
DANN	Benign	0.59
PhyloP100		-0.0060
PromoterAI		-0.064	Neutral
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: rs7118396; hg19: chr11-47269936;