rs617182

Variant names:

• chr17-49229912-G-A
• rs617182
• NM_178500.4:c.-68+556C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-49229912-G-A
• chr17-49229912-G-C
• chr17-49229912-G-T

Variant summary

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

The NM_178500.4(PHOSPHO1):​c.-68+556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,958 control chromosomes in the GnomAD database, including 22,900 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 0.53 (22900 hom., cov: 31)
• Consequence: PHOSPHO1 NM_178500.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 15 publications found

Genes affected

PHOSPHO1 (HGNC:16815): (phosphoethanolamine/phosphocholine phosphatase 1) Enables pyrophosphatase activity. Predicted to be involved in bone mineralization involved in bone maturation. Predicted to act upstream of or within endochondral ossification. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

FLJ40194 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178500.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHOSPHO1	NM_178500.4	MANE Select	c.-68+556C>T		intron	N/A	NP_848595.1	Q8TCT1-1
	PHOSPHO1	NM_001143804.2		c.-120+556C>T		intron	N/A	NP_001137276.1	Q8TCT1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHOSPHO1	ENST00000310544.9	TSL:2 MANE Select	c.-68+556C>T		intron	N/A	ENSP00000311925.4	Q8TCT1-1
	PHOSPHO1	ENST00000413580.5	TSL:2	c.-120+556C>T		intron	N/A	ENSP00000406909.1	Q8TCT1-3
	PHOSPHO1	ENST00000511066.5	TSL:2	c.-68+665C>T		intron	N/A	ENSP00000426095.1	D6RHH9

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80957 AN: 151840 Hom.: 22870 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.533 AC: 81029 AN: 151958 Hom.: 22900 Cov.: 31 AF XY: 0.533 AC XY: 39584 AN XY: 74252

African (AFR) AF: 0.722 AC: 29908 AN: 41420

American (AMR) AF: 0.492 AC: 7512 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1891 AN: 5148

South Asian (SAS) AF: 0.673 AC: 3245 AN: 4822

European-Finnish (FIN) AF: 0.454 AC: 4793 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30276 AN: 67946

Other (OTH) AF: 0.499 AC: 1053 AN: 2112

Alfa AF: 0.483 Hom.: 52914

Bravo AF: 0.539

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		-0.16
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: rs617182; hg19: chr17-47307274;