rs10494248

Variant names:

• chr1-147636461-G-A
• rs10494248
• ENST00000609196.5:c.459-5396C>T

Variant summary

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

The ENST00000609196.5(ACP6):​c.459-5396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,112 control chromosomes in the GnomAD database, including 747 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 0.060 (747 hom., cov: 32)
• Consequence: ACP6 ENST00000609196.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 3 publications found

Genes affected

ACP6 (HGNC:29609): (acid phosphatase 6, lysophosphatidic) This gene encodes a member of the histidine acid phosphatase protein family. The encoded protein hydrolyzes lysophosphatidic acid, which is involved in G protein-coupled receptor signaling, lipid raft modulation, and in balancing lipid composition within the cell. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP6	XM_011509601.4	c.1144-5396C>T		intron_variant	Intron 9 of 9		XP_011507903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP6	ENST00000609196.5	c.459-5396C>T		intron_variant	Intron 5 of 5	3		ENSP00000477476.2

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9162 AN: 151994 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.00745

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00929

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0604 AC: 9182 AN: 152112 Hom.: 747 Cov.: 32 AF XY: 0.0590 AC XY: 4384 AN XY: 74368

African (AFR) AF: 0.190 AC: 7855 AN: 41446

American (AMR) AF: 0.0239 AC: 366 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5162

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4826

European-Finnish (FIN) AF: 0.00745 AC: 79 AN: 10598

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.00929 AC: 632 AN: 68008

Other (OTH) AF: 0.0365 AC: 77 AN: 2110

Alfa AF: 0.0503 Hom.: 101

Bravo AF: 0.0668

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.63
PhyloP100		-0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10494248; hg19: chr1-147108260;