rs1344

Variant names:

• chr1-147647471-G-A
• rs1344
• NM_016361.5:c.1239C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-147647471-G-A
• chr1-147647471-G-C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642
• Publications: 56 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 -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 rank	MANE	Protein	UniProt
ACP6	NM_016361.5	c.1239C>T	p.His413His	synonymous_variant	Exon 10 of 10	ENST00000583509.7	NP_057445.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP6	ENST00000583509.7	c.1239C>T	p.His413His	synonymous_variant	Exon 10 of 10	1	NM_016361.5	ENSP00000463574.1
ACP6	ENST00000613673.4	n.4461C>T		non_coding_transcript_exon_variant	Exon 8 of 8	1
ACP6	ENST00000460583.1	n.802C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
ACP6	ENST00000609196.5	c.458+2672C>T		intron_variant	Intron 5 of 5	3		ENSP00000477476.2

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

GnomAD2 exomes AF: 0.541 AC: 135915 AN: 251252 AF XY: 0.534

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 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

African (AFR) AF: 0.454 AC: 15198 AN: 33468

American (AMR) AF: 0.638 AC: 28535 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 15246 AN: 26136

East Asian (EAS) AF: 0.407 AC: 16144 AN: 39688

South Asian (SAS) AF: 0.409 AC: 35251 AN: 86240

European-Finnish (FIN) AF: 0.582 AC: 31060 AN: 53326

Middle Eastern (MID) AF: 0.505 AC: 2911 AN: 5768

European-Non Finnish (NFE) AF: 0.573 AC: 636934 AN: 1111808

Other (OTH) AF: 0.541 AC: 32683 AN: 60380

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

African (AFR) AF: 0.461 AC: 19114 AN: 41466

American (AMR) AF: 0.596 AC: 9122 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2038 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1964 AN: 5164

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4822

European-Finnish (FIN) AF: 0.580 AC: 6124 AN: 10550

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39262 AN: 67972

Other (OTH) AF: 0.543 AC: 1150 AN: 2116

Alfa AF: 0.559 Hom.: 88996

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
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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