rs472265

Variant names:

• chr19-39090097-A-G
• rs472265
• NM_001004318.3:c.121+4707A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-39090097-A-G
• chr19-39090097-A-T

Variant summary

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

The NM_001004318.3(ACP7):​c.121+4707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,050 control chromosomes in the GnomAD database, including 3,777 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 0.22 (3777 hom., cov: 32)
• Consequence: ACP7 NM_001004318.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 28 publications found

Genes affected

ACP7 (HGNC:33781): (acid phosphatase 7, tartrate resistant (putative)) Purple acid phosphatases (PAPs), including PAPL, are a family of binuclear metallohydrolases that have been identified in plants, animals, and fungi (Flanagan et al., 2006 [PubMed 16793224]).[supplied by OMIM, Mar 2008]

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 = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP7	NM_001004318.3	c.121+4707A>G		intron_variant	Intron 2 of 12	ENST00000331256.10	NP_001004318.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP7	ENST00000331256.10	c.121+4707A>G		intron_variant	Intron 2 of 12	2	NM_001004318.3	ENSP00000327557.4
ACP7	ENST00000594229.1	c.121+4707A>G		intron_variant	Intron 1 of 9	5		ENSP00000470989.1
ACP7	ENST00000601575.5	n.121+4707A>G		intron_variant	Intron 2 of 10	2		ENSP00000469048.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33804 AN: 151932 Hom.: 3769 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.223 AC: 33852 AN: 152050 Hom.: 3777 Cov.: 32 AF XY: 0.222 AC XY: 16479 AN XY: 74328

African (AFR) AF: 0.245 AC: 10169 AN: 41460

American (AMR) AF: 0.191 AC: 2914 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5174

South Asian (SAS) AF: 0.207 AC: 996 AN: 4814

European-Finnish (FIN) AF: 0.217 AC: 2299 AN: 10590

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14288 AN: 67972

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.213 Hom.: 16760

Bravo AF: 0.226

Asia WGS AF: 0.260 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.43
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: rs472265; hg19: chr19-39580737;