GeneBe

rs2252641

Variant names:

Variant summary

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

The ENST00000445791.5(TEX41):​n.308-26926T>A 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: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TEX41
ENST00000445791.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.54

Publications

0 publications found
Variant links:
Genes affected
TEX41 (HGNC:48667): (testis expressed 41)

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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=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TEX41NR_033870.2 linkn.464-26926T>A intron_variant Intron 3 of 4
LOC100505498XR_923410.3 linkn.5785+20621T>A intron_variant Intron 3 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TEX41ENST00000445791.5 linkn.308-26926T>A intron_variant Intron 2 of 3 1
TEX41ENST00000451774.5 linkn.405-26926T>A intron_variant Intron 3 of 4 1
TEX41ENST00000597173.6 linkn.433+20621T>A intron_variant Intron 1 of 1 1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
14
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
14
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
10
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.062
DANN
Benign
0.47
PhyloP100
-4.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs2252641; hg19: chr2-145801461; API