5-109885325-C-T

Variant names:

• chr5-109885325-C-T
• rs112724034
• ENST00000518923.1:n.99G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

PGAM5P1 (HGNC:42467): (PGAM family member 5, mitochondrial serine/threonine protein phosphatase pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518923.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGAM5P1	ENST00000518923.1	TSL:6	n.99G>A		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.0636 AC: 7 AN: 110

American (AMR) AF: 0.0117 AC: 7 AN: 600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 124

East Asian (EAS) AF: 0.00 AC: 0 AN: 192

South Asian (SAS) AF: 0.0389 AC: 53 AN: 1364

European-Finnish (FIN) AF: 0.0479 AC: 23 AN: 480

Middle Eastern (MID) AF: 0.0152 AC: 2 AN: 132

European-Non Finnish (NFE) AF: 0.0374 AC: 218 AN: 5826

Other (OTH) AF: 0.0317 AC: 14 AN: 442

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

African (AFR) AF: 0.120 AC: 5009 AN: 41580

American (AMR) AF: 0.0319 AC: 488 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3472

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5168

South Asian (SAS) AF: 0.0565 AC: 273 AN: 4832

European-Finnish (FIN) AF: 0.0402 AC: 427 AN: 10624

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0370 AC: 2518 AN: 68014

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0423 Hom.: 276

Bravo AF: 0.0602

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.79
PhyloP100		0.043

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs112724034;

hg19: chr5-109221026;