19-9834503-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The NR_183873.1(PIN1-DT):n.328C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,298 control chromosomes in the GnomAD database, including 2,147 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely pathogenic (no stars).

• Frequency:
  • Genomes: 𝑓 0.15 (2144 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3 hom.)
• Consequence: PIN1-DT NR_183873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

PIN1-DT (HGNC:55303): (PIN1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 19-9834503-G-C is Pathogenic according to our data. Variant chr19-9834503-G-C is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).. Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIN1-DT	NR_183873.1	n.328C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIN1-DT	ENST00000591174.1	n.326C>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22385 AN: 151910 Hom.: 2144 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.122 AC: 33 AN: 270 Hom.: 3 Cov.: 0 AF XY: 0.138 AC XY: 19 AN XY: 138

Gnomad4 AFR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0417

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.0500

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.147 AC: 22402 AN: 152028 Hom.: 2144 Cov.: 32 AF XY: 0.146 AC XY: 10820 AN XY: 74312

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0331

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0527 Hom.: 52

Bravo AF: 0.151

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.7
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: rs2233678; hg19: chr19-9945179;