rs12461917

Positions:

• chr19-46614145-C-A
• chr19-46614145-C-T

Variant summary

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

The XR_243945.4(PTGIR):​n.1097+47G>T 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 0.154 in 152,192 control chromosomes in the GnomAD database, including 2,070 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 0.15 (2070 hom., cov: 32)
• Consequence: PTGIR XR_243945.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

Genes affected

PTGIR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGIR	XR_243945.4	n.1097+47G>T		intron_variant, non_coding_transcript_variant
PTGIR	XR_430206.4	n.1097+47G>T		intron_variant, non_coding_transcript_variant
PTGIR	XR_935844.3	n.1097+47G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23438 AN: 152074 Hom.: 2072 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.154 AC: 23447 AN: 152192 Hom.: 2070 Cov.: 32 AF XY: 0.155 AC XY: 11519 AN XY: 74400

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0923

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.139

Alfa AF: 0.117 Hom.: 431

Bravo AF: 0.151

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12461917; hg19: chr19-47117402;