rs10510876

chr3-62299466-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_038281.1(PTPRG-AS1):n.176-4688G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 152,242 control chromosomes in the GnomAD database, including 28 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 0.016 (28 hom., cov: 32)
• Consequence: PTPRG-AS1 NR_038281.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

PTPRG-AS1 (HGNC:44638): (PTPRG antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0156 (2379/152242) while in subpopulation EAS AF= 0.0499 (258/5170). AF 95% confidence interval is 0.0449. There are 28 homozygotes in gnomad4. There are 1151 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 27 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPRG-AS1	NR_038281.1	n.176-4688G>C		intron_variant, non_coding_transcript_variant
PTPRG-AS1	NR_038282.1	n.266-4688G>C		intron_variant, non_coding_transcript_variant
PTPRG-AS1	NR_038283.1	n.262+17640G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPRG-AS1	ENST00000665590.1	n.235-4688G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0156 AC: 2372 AN: 152124 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.00478

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.00726

Gnomad FIN AF: 0.00519

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0156 AC: 2379 AN: 152242 Hom.: 28 Cov.: 32 AF XY: 0.0155 AC XY: 1151 AN XY: 74422

Gnomad4 AFR AF: 0.00476

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.00726

Gnomad4 FIN AF: 0.00519

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0151 Hom.: 1

Bravo AF: 0.0185

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	9.1
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510876; hg19: chr3-62285141;