ENST00000626376.2:n.220-31700A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 88 publications found

Genes affected

PGAM1P5 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.201 AC: 8341 AN: 41522

American (AMR) AF: 0.343 AC: 5233 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1327 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1377 AN: 4806

European-Finnish (FIN) AF: 0.353 AC: 3734 AN: 10580

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20382 AN: 67978

Other (OTH) AF: 0.296 AC: 625 AN: 2108

Alfa AF: 0.288 Hom.: 18309

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17356907; hg19: chr12-96027759;