rs10510876

Variant names:

• chr3-62299466-C-G
• rs10510876
• ENST00000474795.5:n.263-4688G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000474795.5(PTPRG-AS1):​n.263-4688G>C variant causes a intron 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 ENST00000474795.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRG-AS1	NR_038281.1	n.176-4688G>C		intron_variant	Intron 2 of 4
PTPRG-AS1	NR_038282.1	n.266-4688G>C		intron_variant	Intron 3 of 4
PTPRG-AS1	NR_038283.1	n.262+17640G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRG-AS1	ENST00000474795.5	n.263-4688G>C		intron_variant	Intron 3 of 4	1
PTPRG-AS1	ENST00000479018.5	n.164-4688G>C		intron_variant	Intron 2 of 4	1
PTPRG-AS1	ENST00000462497.5	n.238+17640G>C		intron_variant	Intron 3 of 3	2

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

African (AFR) AF: 0.00476 AC: 198 AN: 41558

American (AMR) AF: 0.0389 AC: 595 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3472

East Asian (EAS) AF: 0.0499 AC: 258 AN: 5170

South Asian (SAS) AF: 0.00726 AC: 35 AN: 4820

European-Finnish (FIN) AF: 0.00519 AC: 55 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1114 AN: 68022

Other (OTH) AF: 0.0142 AC: 30 AN: 2116

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
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10510876; hg19: chr3-62285141;