rs1344

chr1-147647471-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_016361.5(ACP6):c.1239C>T(p.His413=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,613,580 control chromosomes in the GnomAD database, including 251,247 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 0.54 (22161 hom., cov: 33)
  • Exomes 𝑓: 0.56 (229086 hom.)
• Consequence: ACP6 NM_016361.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP7: Synonymous conserved (PhyloP=0.642 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACP6	NM_016361.5	c.1239C>T	p.His413=	synonymous_variant	10/10	ENST00000583509.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACP6	ENST00000583509.7	c.1239C>T	p.His413=	synonymous_variant	10/10	1	NM_016361.5	P1
ACP6	ENST00000613673.4	n.4461C>T		non_coding_transcript_exon_variant	8/8	1
ACP6	ENST00000609196.5	c.460+2672C>T		intron_variant		3
ACP6	ENST00000460583.1	n.802C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81289 AN: 151938 Hom.: 22135 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.544

GnomAD3 exomes AF: 0.541 AC: 135915 AN: 251252 Hom.: 37657 AF XY: 0.534 AC XY: 72519 AN XY: 135798

Gnomad AFR exome AF: 0.455

Gnomad AMR exome AF: 0.641

Gnomad ASJ exome AF: 0.581

Gnomad EAS exome AF: 0.364

Gnomad SAS exome AF: 0.409

Gnomad FIN exome AF: 0.579

Gnomad NFE exome AF: 0.575

Gnomad OTH exome AF: 0.553

GnomAD4 exome AF: 0.557 AC: 813962 AN: 1461524 Hom.: 229086 Cov.: 52 AF XY: 0.552 AC XY: 401538 AN XY: 727092

Gnomad4 AFR exome AF: 0.454

Gnomad4 AMR exome AF: 0.638

Gnomad4 ASJ exome AF: 0.583

Gnomad4 EAS exome AF: 0.407

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.582

Gnomad4 NFE exome AF: 0.573

Gnomad4 OTH exome AF: 0.541

GnomAD4 genome AF: 0.535 AC: 81372 AN: 152056 Hom.: 22161 Cov.: 33 AF XY: 0.534 AC XY: 39661 AN XY: 74318

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.543

Alfa AF: 0.563 Hom.: 57727

Bravo AF: 0.534

Asia WGS AF: 0.393 AC: 1368 AN: 3478

EpiCase AF: 0.572

EpiControl AF: 0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.0
Dann	Benign	0.42

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: rs1344; hg19: chr1-147119273; COSMIC: COSV65077013; COSMIC: COSV65077013;