rs1929494

chr9-101474492-G-Achr9-101474492-G-T

Variant summary

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

The NM_032342.3(PGAP4):c.*1389C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,082 control chromosomes in the GnomAD database, including 12,576 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 0.40 (12575 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: PGAP4 NM_032342.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

Genes affected

PGAP4 (HGNC:28180): (post-GPI attachment to proteins GalNAc transferase 4) Enables glycosyltransferase activity. Involved in GPI anchor biosynthetic process. Located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM246-AS1 (HGNC:51191): (TMEM246 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGAP4	NM_032342.3	c.*1389C>T		3_prime_UTR_variant	2/2	ENST00000374848.8
TMEM246-AS1	NR_121573.1	n.171-384G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGAP4	ENST00000374848.8	c.*1389C>T		3_prime_UTR_variant	2/2	1	NM_032342.3	P1
TMEM246-AS1	ENST00000424154.6	n.212-5348G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60240 AN: 151960 Hom.: 12563 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.396 AC: 60274 AN: 152078 Hom.: 12575 Cov.: 33 AF XY: 0.403 AC XY: 29924 AN XY: 74328

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.399

Alfa AF: 0.430 Hom.: 19192

Bravo AF: 0.377

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.9
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1929494; hg19: chr9-104236774;