19-39090097-A-G

Position:

• chr19-39090097-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ACP7	NM_001004318.3	c.121+4707A>G		intron_variant		ENST00000331256.10	NP_001004318.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACP7	ENST00000331256.10	c.121+4707A>G		intron_variant		2	NM_001004318.3	ENSP00000327557	P1
ACP7	ENST00000594229.1	c.121+4707A>G		intron_variant		5		ENSP00000470989
ACP7	ENST00000601575.5	c.121+4707A>G		intron_variant, NMD_transcript_variant		2		ENSP00000469048

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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.218

Alfa AF: 0.211 Hom.: 8016

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

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: rs472265; hg19: chr19-39580737;