rs2233680

Variant names:

• chr19-9834693-A-G
• rs2233680
• ENST00000591174.2:n.285-15T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000591174.2(PIN1-DT):​n.285-15T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PIN1-DT ENST00000591174.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIN1-DT	NR_183873.1	n.153-15T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIN1-DT	ENST00000591174.2	n.285-15T>C		intron_variant	Intron 1 of 1	3
PIN1-DT	ENST00000731112.1	n.154-15T>C		intron_variant	Intron 1 of 3
PIN1-DT	ENST00000731113.1	n.240-15T>C		intron_variant	Intron 1 of 1
PIN1-DT	ENST00000731114.1	n.248-15T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 7574 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3952

African (AFR) AF: 0.00 AC: 0 AN: 228

American (AMR) AF: 0.00 AC: 0 AN: 152

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 200

East Asian (EAS) AF: 0.00 AC: 0 AN: 904

South Asian (SAS) AF: 0.00 AC: 0 AN: 208

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 762

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 24

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4682

Other (OTH) AF: 0.00 AC: 0 AN: 414

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2233680; hg19: chr19-9945369;