rs200040694

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001127202.4(PCID2):​c.1111-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000549 in 1,458,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

PCID2
NM_001127202.4 splice_region, intron

Scores

2
Splicing: ADA: 0.00001308
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08
Variant links:
Genes affected
PCID2 (HGNC:25653): (PCI domain containing 2) This gene encodes a component of the TREX-2 complex (transcription and export complex 2), which regulates mRNA export from the nucleus. This protein regulates expression of Mad2 mitotic arrest deficient-like 1, a cell division checkpoint protein. This protein also interacts with and stabilizes Brca2 (breast cancer 2) protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCID2NM_001127202.4 linkc.1111-4G>T splice_region_variant, intron_variant Intron 13 of 13 ENST00000337344.9 NP_001120674.1 Q5JVF3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCID2ENST00000337344.9 linkc.1111-4G>T splice_region_variant, intron_variant Intron 13 of 13 2 NM_001127202.4 ENSP00000337405.4 Q5JVF3-1
PCID2ENST00000375477.5 linkc.1111-4G>T splice_region_variant, intron_variant Intron 13 of 14 1 ENSP00000364626.1 Q5JVF3-1
PCID2ENST00000375479.6 linkc.1111-4G>T splice_region_variant, intron_variant Intron 13 of 14 2 ENSP00000364628.2 Q5JVF3-1
PCID2ENST00000375457.2 linkc.1105-4G>T splice_region_variant, intron_variant Intron 13 of 13 1 ENSP00000364606.2 Q5JVF3-2
PCID2ENST00000375459.5 linkc.1105-4G>T splice_region_variant, intron_variant Intron 13 of 14 2 ENSP00000364608.1 Q5JVF3-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000549
AC:
8
AN:
1458124
Hom.:
0
Cov.:
28
AF XY:
0.00000689
AC XY:
5
AN XY:
725656
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000721
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.089
DANN
Benign
0.56
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000013
dbscSNV1_RF
Benign
0.0060
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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200040694; hg19: chr13-113832605; API