rs1953977

chr1-147636673-G-Achr1-147636673-G-Cchr1-147636673-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609196.5(ACP6):c.461-5608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0928 in 152,182 control chromosomes in the GnomAD database, including 1,932 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 0.093 (1932 hom., cov: 32)
• Consequence: ACP6 ENST00000609196.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACP6	XM_011509601.4	c.1144-5608C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACP6	ENST00000609196.5	c.461-5608C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14084 AN: 152064 Hom.: 1927 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.00745

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00995

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0928 AC: 14116 AN: 152182 Hom.: 1932 Cov.: 32 AF XY: 0.0888 AC XY: 6606 AN XY: 74404

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.00745

Gnomad4 NFE AF: 0.00995

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0147 Hom.: 30

Bravo AF: 0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953977; hg19: chr1-147108472;