GeneBe

rs373161176

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001370215.1(ZNF71):​c.257C>G​(p.Thr86Arg) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. 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. T86M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

ZNF71
NM_001370215.1 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.83

Publications

0 publications found
Variant links:
Genes affected
ZNF71 (HGNC:13141): (zinc finger protein 71) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
ZIM2-AS1 (HGNC:51304): (ZIM2 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06968379).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370215.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ZNF71
NM_001370215.1
MANE Select
c.257C>Gp.Thr86Arg
missense
Exon 4 of 4NP_001357144.1M0R0C0
ZNF71
NM_001370214.1
c.77C>Gp.Thr26Arg
missense
Exon 3 of 3NP_001357143.1Q9NQZ8
ZNF71
NM_021216.5
c.77C>Gp.Thr26Arg
missense
Exon 3 of 3NP_067039.1Q9NQZ8

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ZNF71
ENST00000599599.7
TSL:2 MANE Select
c.257C>Gp.Thr86Arg
missense
Exon 4 of 4ENSP00000471138.2M0R0C0
ZNF71
ENST00000328070.10
TSL:1
c.77C>Gp.Thr26Arg
missense
Exon 3 of 3ENSP00000328245.5Q9NQZ8
ENSG00000293626
ENST00000716550.1
n.160+7426C>G
intron
N/AENSP00000520562.1A0ABB0MV33

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.00000433
AC:
1
AN:
231184
AF XY:
0.00000803
show subpopulations
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:
0.00000950
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.69
CADD
Benign
0.017
DANN
Benign
0.93
DEOGEN2
Benign
0.023
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.028
N
LIST_S2
Benign
0.15
T
M_CAP
Benign
0.0020
T
MetaRNN
Benign
0.070
T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.55
N
PhyloP100
-4.8
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-0.28
N
REVEL
Benign
0.027
Sift
Benign
0.46
T
Sift4G
Benign
0.37
T
Polyphen
0.0020
B
Vest4
0.15
MutPred
0.25
Loss of glycosylation at T26 (P = 0.0169)
MVP
0.014
MPC
0.42
ClinPred
0.049
T
GERP RS
-2.2
Varity_R
0.055
gMVP
0.081
Mutation Taster
=100/0
polymorphism

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: rs373161176; hg19: chr19-57132732; API