19-9834678-C-T

Position:

• chr19-9834678-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000591174.1(PIN1-DT):​n.151G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 159,650 control chromosomes in the GnomAD database, including 28,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.59 (27499 hom., cov: 32)
  • Exomes 𝑓: 0.57 (1302 hom.)
• Consequence: PIN1-DT ENST00000591174.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

Genes affected

PIN1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 19-9834678-C-T is Benign according to our data. Variant chr19-9834678-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIN1-DT	NR_183873.1	n.153G>A		splice_region_variant, non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIN1-DT	ENST00000591174.1	n.151G>A		splice_region_variant, non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89948 AN: 151858 Hom.: 27499 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.568 AC: 4358 AN: 7674 Hom.: 1302 Cov.: 0 AF XY: 0.571 AC XY: 2303 AN XY: 4034

Gnomad4 AFR exome AF: 0.450

Gnomad4 AMR exome AF: 0.575

Gnomad4 ASJ exome AF: 0.668

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.632

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 0.573

GnomAD4 genome AF: 0.592 AC: 89991 AN: 151976 Hom.: 27499 Cov.: 32 AF XY: 0.589 AC XY: 43729 AN XY: 74248

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.600

Alfa AF: 0.654 Hom.: 63239

Bravo AF: 0.591

Asia WGS AF: 0.427 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233679; hg19: chr19-9945354;