19-9834678-C-T

Variant names:

• chr19-9834678-C-T
• rs2233679
• ENST00000591174.2:n.285G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591174.2(PIN1-DT):​n.285G>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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.59 (27499 hom., cov: 32)
  • Exomes 𝑓: 0.57 (1302 hom.)
• Consequence: PIN1-DT ENST00000591174.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 51 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591174.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIN1-DT	NR_183873.1		n.153G>A		splice_region non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIN1-DT	ENST00000591174.2	TSL:3	n.285G>A		splice_region non_coding_transcript_exon	Exon 2 of 2
	PIN1-DT	ENST00000731112.1		n.154G>A		splice_region non_coding_transcript_exon	Exon 2 of 4
	PIN1-DT	ENST00000731113.1		n.240G>A		splice_region non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.450 AC: 109 AN: 242

American (AMR) AF: 0.575 AC: 92 AN: 160

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 151 AN: 226

East Asian (EAS) AF: 0.333 AC: 318 AN: 954

South Asian (SAS) AF: 0.404 AC: 72 AN: 178

European-Finnish (FIN) AF: 0.632 AC: 517 AN: 818

Middle Eastern (MID) AF: 0.583 AC: 14 AN: 24

European-Non Finnish (NFE) AF: 0.611 AC: 2843 AN: 4650

Other (OTH) AF: 0.573 AC: 242 AN: 422

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

African (AFR) AF: 0.466 AC: 19309 AN: 41432

American (AMR) AF: 0.661 AC: 10092 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2030 AN: 5160

South Asian (SAS) AF: 0.447 AC: 2157 AN: 4822

European-Finnish (FIN) AF: 0.632 AC: 6671 AN: 10548

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45448 AN: 67970

Other (OTH) AF: 0.600 AC: 1267 AN: 2110

Alfa AF: 0.640 Hom.: 94257

Bravo AF: 0.591

Asia WGS AF: 0.427 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2233679; hg19: chr19-9945354;