chr9-101474492-G-A

Variant names:

• chr9-101474492-G-A
• rs1929494
• NM_032342.3:c.*1389C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032342.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGAP4	NM_032342.3	MANE Select	c.*1389C>T		3_prime_UTR	Exon 2 of 2	NP_115718.1
	PGAP4	NM_001303107.2		c.*1389C>T		3_prime_UTR	Exon 3 of 3	NP_001290036.1
	PGAP4	NM_001303108.2		c.*1389C>T		3_prime_UTR	Exon 2 of 2	NP_001290037.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGAP4	ENST00000374848.8	TSL:1 MANE Select	c.*1389C>T		3_prime_UTR	Exon 2 of 2	ENSP00000363981.3
	PGAP4	ENST00000374851.1	TSL:1	c.*1389C>T		3_prime_UTR	Exon 4 of 4	ENSP00000363984.1
	PGAP4	ENST00000374847.5	TSL:3	c.*1389C>T		3_prime_UTR	Exon 3 of 3	ENSP00000363980.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.267 AC: 11084 AN: 41482

American (AMR) AF: 0.382 AC: 5835 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5162

South Asian (SAS) AF: 0.504 AC: 2428 AN: 4818

European-Finnish (FIN) AF: 0.494 AC: 5225 AN: 10578

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30418 AN: 67974

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.425 Hom.: 23677

Bravo AF: 0.377

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		0.050
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1929494; hg19: chr9-104236774;