chr5-109885325-C-T

Position:

• chr5-109885325-C-T

Variant summary

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

The ENST00000518923.1(PGAM5P1):​n.99G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 161,588 control chromosomes in the GnomAD database, including 402 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 0.059 (394 hom., cov: 34)
  • Exomes 𝑓: 0.035 (8 hom.)
• Consequence: PGAM5P1 ENST00000518923.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

PGAM5P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGAM5P1		n.109885325C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGAM5P1	ENST00000518923.1	n.99G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8948 AN: 152200 Hom.: 388 Cov.: 34

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0598

GnomAD4 exome AF: 0.0350 AC: 324 AN: 9270 Hom.: 8 Cov.: 0 AF XY: 0.0346 AC XY: 192 AN XY: 5544

Gnomad4 AFR exome AF: 0.0636

Gnomad4 AMR exome AF: 0.0117

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0389

Gnomad4 FIN exome AF: 0.0479

Gnomad4 NFE exome AF: 0.0374

Gnomad4 OTH exome AF: 0.0317

GnomAD4 genome AF: 0.0590 AC: 8993 AN: 152318 Hom.: 394 Cov.: 34 AF XY: 0.0586 AC XY: 4363 AN XY: 74474

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0520 Hom.: 33

Bravo AF: 0.0602

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112724034; hg19: chr5-109221026;