GeneBe

rs370050204

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005425.5(TNP2):​c.4G>T​(p.Asp2Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D2N) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

TNP2
NM_005425.5 missense

Scores

3
10
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.02

Publications

1 publications found
Variant links:
Genes affected
TNP2 (HGNC:11952): (transition protein 2) Predicted to enable zinc ion binding activity. Predicted to be involved in positive regulation of protein processing; single fertilization; and spermatogenesis, exchange of chromosomal proteins. Predicted to act upstream of or within binding activity of sperm to zona pellucida and flagellated sperm motility. Predicted to be located in nucleus. Predicted to be part of nucleosome. [provided by Alliance of Genome Resources, Apr 2022]
RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005425.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TNP2
NM_005425.5
MANE Select
c.4G>Tp.Asp2Tyr
missense
Exon 1 of 2NP_005416.1Q05952

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TNP2
ENST00000312693.4
TSL:1 MANE Select
c.4G>Tp.Asp2Tyr
missense
Exon 1 of 2ENSP00000325738.3Q05952
RMI2
ENST00000572173.1
TSL:1
c.-516+19481C>A
intron
N/AENSP00000461206.1Q96E14-2
TNP2
ENST00000560751.1
TSL:6
c.4G>Tp.Asp2Tyr
missense
Exon 1 of 1ENSP00000496261.1A0A2R8Y7P0

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
237178
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.38
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.32
T
M_CAP
Benign
0.039
D
MetaRNN
Uncertain
0.73
D
MetaSVM
Benign
-0.29
T
MutationAssessor
Benign
1.9
L
PhyloP100
3.0
PrimateAI
Uncertain
0.50
T
PROVEAN
Pathogenic
-8.1
D
REVEL
Uncertain
0.47
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.73
MutPred
0.63
Loss of glycosylation at T3 (P = 0.1186)
MVP
0.76
MPC
0.45
ClinPred
1.0
D
GERP RS
3.5
PromoterAI
0.023
Neutral
Varity_R
0.82
gMVP
0.35

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: rs370050204; hg19: chr16-11363116; API