rs1953977

Variant names:

• chr1-147636673-G-A
• rs1953977
• ENST00000609196.5:c.459-5608C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-147636673-G-A
• chr1-147636673-G-C
• chr1-147636673-G-T

Variant summary

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

The ENST00000609196.5(ACP6):​c.459-5608C>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
• Publications: 1 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=-0.89).
• 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 rank	MANE	Protein	UniProt
ACP6	XM_011509601.4	c.1144-5608C>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.459-5608C>T		intron_variant	Intron 5 of 5	3		ENSP00000477476.2

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

African (AFR) AF: 0.302 AC: 12527 AN: 41486

American (AMR) AF: 0.0340 AC: 520 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4826

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

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00995 AC: 677 AN: 68014

Other (OTH) AF: 0.0627 AC: 132 AN: 2104

Alfa AF: 0.0248 Hom.: 65

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1953977; hg19: chr1-147108472;