rs12115722

chr9-131553120-G-T

Variant summary

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

The NM_001395643.1(PRRT1B):c.26-1437G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,104 control chromosomes in the GnomAD database, including 800 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 0.090 (800 hom., cov: 31)
• Consequence: PRRT1B NM_001395643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

PRRT1B (HGNC:53642): (proline rich transmembrane protein 1B) Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRRT1B	NM_001395643.1	c.26-1437G>T		intron_variant		ENST00000636672.2
PRRT1B	NM_001365666.1	c.41-1437G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRRT1B	ENST00000636672.2	c.26-1437G>T		intron_variant		5	NM_001395643.1	P1

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13701 AN: 151986 Hom.: 798 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0902 AC: 13715 AN: 152104 Hom.: 800 Cov.: 31 AF XY: 0.0900 AC XY: 6694 AN XY: 74376

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0668 Hom.: 257

Bravo AF: 0.0997

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.98
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12115722; hg19: chr9-134428507;