19-9834111-G-C

Position:

• chr19-9834111-G-C

Variant summary

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

The NR_183873.1(PIN1-DT):​n.720C>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 0.801 in 152,114 control chromosomes in the GnomAD database, including 49,627 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 0.80 (49624 hom., cov: 31)
  • Exomes 𝑓: 0.67 (3 hom.)
• Consequence: PIN1-DT NR_183873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIN1-DT	NR_183873.1	n.720C>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.718C>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121798 AN: 151984 Hom.: 49592 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 0.667 AC: 8 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.801 AC: 121890 AN: 152102 Hom.: 49624 Cov.: 31 AF XY: 0.796 AC XY: 59201 AN XY: 74338

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.812

Alfa AF: 0.738 Hom.: 2181

Bravo AF: 0.815

Asia WGS AF: 0.591 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804459; hg19: chr19-9944787;