rs17356907

Variant names:

• chr12-95633983-A-G
• rs17356907
• ENST00000626376.2:n.220-31700A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626376.2(PGAM1P5):​n.220-31700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,116 control chromosomes in the GnomAD database, including 6,267 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 0.28 (6267 hom., cov: 32)
• Consequence: PGAM1P5 ENST00000626376.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

PGAM1P5 (HGNC:42452): (phosphoglycerate mutase 1 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGAM1P5	ENST00000626376.2	n.220-31700A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42352 AN: 152000 Hom.: 6268 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.278 AC: 42346 AN: 152116 Hom.: 6267 Cov.: 32 AF XY: 0.282 AC XY: 20957 AN XY: 74364

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.296

Alfa AF: 0.272 Hom.: 549

Bravo AF: 0.274

Asia WGS AF: 0.259 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17356907; hg19: chr12-96027759;