chr19-9842067-G-A

Variant names:

• chr19-9842067-G-A
• rs1985604
• NM_006221.4:c.271+3419G>A

Variant summary

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

The NM_006221.4(PIN1):​c.271+3419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 152,224 control chromosomes in the GnomAD database, including 859 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 0.098 (859 hom., cov: 33)
• Consequence: PIN1 NM_006221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 3 publications found

Genes affected

PIN1 (HGNC:8988): (peptidylprolyl cis/trans isomerase, NIMA-interacting 1) Peptidyl-prolyl cis/trans isomerases (PPIases) catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds. This gene encodes one of the PPIases, which specifically binds to phosphorylated ser/thr-pro motifs to catalytically regulate the post-phosphorylation conformation of its substrates. The conformational regulation catalyzed by this PPIase has a profound impact on key proteins involved in the regulation of cell growth, genotoxic and other stress responses, the immune response, induction and maintenance of pluripotency, germ cell development, neuronal differentiation, and survival. This enzyme also plays a key role in the pathogenesis of Alzheimer's disease and many cancers. Multiple alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jun 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006221.4. 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	NM_006221.4	MANE Select	c.271+3419G>A		intron	N/A	NP_006212.1
	PIN1	NR_038422.3		n.351+3419G>A		intron	N/A
	PIN1	NR_038830.2		n.351+3419G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIN1	ENST00000247970.9	TSL:1 MANE Select	c.271+3419G>A		intron	N/A	ENSP00000247970.5
	PIN1	ENST00000380889.6	TSL:1	n.1304+3419G>A		intron	N/A
	PIN1	ENST00000588695.5	TSL:2	c.271+3419G>A		intron	N/A	ENSP00000466962.1

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14867 AN: 152106 Hom.: 861 Cov.: 33

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.111

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0976 AC: 14858 AN: 152224 Hom.: 859 Cov.: 33 AF XY: 0.0981 AC XY: 7302 AN XY: 74424

African (AFR) AF: 0.0492 AC: 2045 AN: 41542

American (AMR) AF: 0.0855 AC: 1308 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3470

East Asian (EAS) AF: 0.0969 AC: 501 AN: 5170

South Asian (SAS) AF: 0.142 AC: 687 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8281 AN: 67988

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.0280 Hom.: 23

Bravo AF: 0.0936

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.61
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1985604; hg19: chr19-9952743;