rs1610874

Variant names:

• chr16-2212926-G-GT
• rs1610874
• NM_001042371.3:c.*801_*802insA

Your query was ambiguous. Multiple possible variants found:

• chr16-2212926-G-GT
• chr16-2212926-G-GTTTA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001042371.3(PGP):​c.*801_*802insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 35)
• Consequence: PGP NM_001042371.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

PGP (HGNC:8909): (phosphoglycolate phosphatase) Enables glycerol-3-phosphatase activity and phosphoglycolate phosphatase activity. Involved in glycerol biosynthetic process; glycerophospholipid metabolic process; and negative regulation of gluconeogenesis. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000261532 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PGP	NM_001042371.3	c.*801_*802insA		3_prime_UTR_variant	Exon 2 of 2	ENST00000333503.8	NP_001035830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGP	ENST00000333503	c.*801_*802insA		3_prime_UTR_variant	Exon 2 of 2	1	NM_001042371.3	ENSP00000330918.7
PGP	ENST00000562001.1	n.*148-80_*148-79insA		intron_variant	Intron 1 of 1	2		ENSP00000457909.1
ENSG00000261532	ENST00000561544.1	n.*63_*64insT		downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 6

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs1610874; hg19: chr16-2262927;