Variant rs1344 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_016361.5(ACP6):c.1239C>T(p.His413His) 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.642

Variant links:

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]

ACP6 links:

ACP6 (HGNC:):

ACP6 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
ACP6	NM_016361.5 linkuse as main transcript	c.1239C>T	p.His413His	synonymous_variant	10/10	ENST00000583509.7	NP_057445.4	Q9NPH0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ACP6	ENST00000583509.7 linkuse as main transcript	c.1239C>T	p.His413His	synonymous_variant	10/10	1	NM_016361.5	ENSP00000463574.1	Q9NPH0-1
ACP6	ENST00000613673.4 linkuse as main transcript	n.4461C>T		non_coding_transcript_exon_variant	8/8	1
ACP6	ENST00000609196.5 linkuse as main transcript	c.458+2672C>T		intron_variant		3		ENSP00000477476.2	V9GZ71
ACP6	ENST00000460583.1 linkuse as main transcript	n.802C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

81289

AN:

151938

Hom.:

22135

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.552

AC XY:

401538

AN XY:

727092

show subpopulations

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.:

AF XY:

0.534

AC XY:

39661

AN XY:

74318

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over