12-95633983-A-G

Position:

• chr12-95633983-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGAM1P5	ENST00000626376.2	n.220-31700A>G		intron_variant, non_coding_transcript_variant		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;