ENST00000404529.2:n.204G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000404529.2(SPIN2P1):​n.204G>C variant causes a non coding transcript exon 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: 23)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control

Consequence

SPIN2P1
ENST00000404529.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.58

Publications

3 publications found
Variant links:
Genes affected
SPIN2P1 (HGNC:54967): (SPIN2 family pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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=-0.54).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPIN2P1 n.57069482C>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPIN2P1ENST00000404529.2 linkn.204G>C non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
108696
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
34896
African (AFR)
AF:
0.00
AC:
0
AN:
2305
American (AMR)
AF:
0.00
AC:
0
AN:
9865
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1873
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3795
South Asian (SAS)
AF:
0.00
AC:
0
AN:
11016
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
15523
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1458
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
57819
Other (OTH)
AF:
0.00
AC:
0
AN:
5042
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
13
DANN
Benign
0.38
PhyloP100
1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs204165; hg19: chrX-57095915; API