6-32152121-T-C

Position:

• chr6-32152121-T-C

Variant summary

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

The ENST00000375150.6(PRRT1):​c.-99A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 692,164 control chromosomes in the GnomAD database, including 284,856 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 0.91 (63758 hom., cov: 28)
  • Exomes 𝑓: 0.90 (221098 hom.)
• Consequence: PRRT1 ENST00000375150.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

Genes affected

PRRT1 (HGNC:13943): (proline rich transmembrane protein 1) Enables identical protein binding activity. Predicted to be involved in several processes, including long-term synaptic depression; protein localization to cell surface; and regulation of AMPA receptor activity. Predicted to act upstream of or within several processes, including learning or memory; long-term synaptic potentiation; and synapse organization. Predicted to be located in postsynaptic density membrane and synaptic vesicle membrane. Predicted to be active in glutamatergic synapse and membrane. Predicted to be integral component of postsynaptic 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRRT1	NM_001363780.2	c.-19A>G		5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRRT1	ENST00000375150.6	c.-99A>G		5_prime_UTR_variant	2/6	1

Frequencies

GnomAD3 genomes AF: 0.915 AC: 138815 AN: 151768 Hom.: 63695 Cov.: 28

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.936

GnomAD3 exomes AF: 0.920 AC: 137583 AN: 149528 Hom.: 63558 AF XY: 0.922 AC XY: 74213 AN XY: 80494

Gnomad AFR exome AF: 0.981

Gnomad AMR exome AF: 0.950

Gnomad ASJ exome AF: 0.974

Gnomad EAS exome AF: 0.998

Gnomad SAS exome AF: 0.975

Gnomad FIN exome AF: 0.872

Gnomad NFE exome AF: 0.869

Gnomad OTH exome AF: 0.914

GnomAD4 exome AF: 0.903 AC: 487845 AN: 540278 Hom.: 221098 Cov.: 0 AF XY: 0.907 AC XY: 265167 AN XY: 292286

Gnomad4 AFR exome AF: 0.975

Gnomad4 AMR exome AF: 0.950

Gnomad4 ASJ exome AF: 0.972

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.975

Gnomad4 FIN exome AF: 0.870

Gnomad4 NFE exome AF: 0.870

Gnomad4 OTH exome AF: 0.904

GnomAD4 genome AF: 0.915 AC: 138936 AN: 151886 Hom.: 63758 Cov.: 28 AF XY: 0.917 AC XY: 68023 AN XY: 74210

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.937

Alfa AF: 0.887 Hom.: 92971

Bravo AF: 0.922

Asia WGS AF: 0.982 AC: 3416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131283; hg19: chr6-32119898;