GeneBe

rs1319763

Variant names:

Variant summary

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

The NM_052935.5(NT5C3B):​c.112-266G>C 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: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

NT5C3B
NM_052935.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.174

Publications

15 publications found
Variant links:
Genes affected
NT5C3B (HGNC:28300): (5'-nucleotidase, cytosolic IIIB) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in exonucleolytic catabolism of deadenylated mRNA. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
KLHL10 (HGNC:18829): (kelch like family member 10) The protein encoded by this gene belongs to the kelch repeat-containing family, and contains an N-terminal BTB/POZ domain a BACK domain and six C-terminal kelch repeats. Kelch domains are thought to form a four stranded beta-sheet blade structure that can fold into a beta-propeller domain when multiple kelch repeats are found together. Mutations in this gene have been associated with oligozoospermia in some infertile males. [provided by RefSeq, Jul 2016]
KLHL10 Gene-Disease associations (from GenCC):
  • male infertility with azoospermia or oligozoospermia due to single gene mutation
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • spermatogenic failure 11
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052935.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NT5C3B
NM_052935.5
MANE Select
c.112-266G>C
intron
N/ANP_443167.4
NT5C3B
NR_033464.2
n.254-266G>C
intron
N/A
NT5C3B
NR_033465.2
n.375-266G>C
intron
N/A

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NT5C3B
ENST00000435506.7
TSL:5 MANE Select
c.112-266G>C
intron
N/AENSP00000389948.2
NT5C3B
ENST00000523903.5
TSL:1
n.401-266G>C
intron
N/A
NT5C3B
ENST00000415460.5
TSL:5
c.112-266G>C
intron
N/AENSP00000397742.1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
537522
Hom.:
0
Cov.:
3
AF XY:
0.00
AC XY:
0
AN XY:
291180
African (AFR)
AF:
0.00
AC:
0
AN:
15388
American (AMR)
AF:
0.00
AC:
0
AN:
33680
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19522
East Asian (EAS)
AF:
0.00
AC:
0
AN:
31278
South Asian (SAS)
AF:
0.00
AC:
0
AN:
61584
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
32012
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3966
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
310158
Other (OTH)
AF:
0.00
AC:
0
AN:
29934
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.0
DANN
Benign
0.37
PhyloP100
-0.17
PromoterAI
0.054
Neutral

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

Publications

Other links and lift over

dbSNP: rs1319763; hg19: chr17-39991790; API