NM_001189.4:c.919C>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001189.4(NKX3-2):ā€‹c.919C>Gā€‹(p.Leu307Val) variant causes a missense change. The variant allele was found at a frequency of 0.000123 in 1,607,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.00065 ( 0 hom., cov: 33)
Exomes š‘“: 0.000068 ( 0 hom. )

Consequence

NKX3-2
NM_001189.4 missense

Scores

9
10

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.49
Variant links:
Genes affected
NKX3-2 (HGNC:951): (NK3 homeobox 2) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; negative regulation of chondrocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; embryonic skeletal system development; and intestinal epithelial cell development. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.016193718).
BP6
Variant 4-13542076-G-C is Benign according to our data. Variant chr4-13542076-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1111841.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NKX3-2NM_001189.4 linkc.919C>G p.Leu307Val missense_variant Exon 2 of 2 ENST00000382438.6 NP_001180.1 P78367
NKX3-2XM_047416049.1 linkc.919C>G p.Leu307Val missense_variant Exon 3 of 3 XP_047272005.1
NKX3-2XM_047416050.1 linkc.919C>G p.Leu307Val missense_variant Exon 3 of 3 XP_047272006.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NKX3-2ENST00000382438.6 linkc.919C>G p.Leu307Val missense_variant Exon 2 of 2 1 NM_001189.4 ENSP00000371875.5 P78367

Frequencies

GnomAD3 genomes
AF:
0.000650
AC:
99
AN:
152256
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00231
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000158
AC:
38
AN:
240038
Hom.:
0
AF XY:
0.000138
AC XY:
18
AN XY:
130644
show subpopulations
Gnomad AFR exome
AF:
0.00204
Gnomad AMR exome
AF:
0.000206
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000680
AC:
99
AN:
1455288
Hom.:
0
Cov.:
31
AF XY:
0.0000595
AC XY:
43
AN XY:
722902
show subpopulations
Gnomad4 AFR exome
AF:
0.00234
Gnomad4 AMR exome
AF:
0.000225
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000183
GnomAD4 genome
AF:
0.000650
AC:
99
AN:
152374
Hom.:
0
Cov.:
33
AF XY:
0.000591
AC XY:
44
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.00231
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000254
Hom.:
0
Bravo
AF:
0.000835
ESP6500AA
AF:
0.00227
AC:
10
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000223
AC:
27

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 03, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.16
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.18
T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.50
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.69
T
M_CAP
Uncertain
0.19
D
MetaRNN
Benign
0.016
T
MetaSVM
Uncertain
0.47
D
MutationAssessor
Uncertain
2.1
M
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-1.3
N
REVEL
Uncertain
0.46
Sift
Benign
0.078
T
Sift4G
Benign
0.23
T
Polyphen
1.0
D
Vest4
0.28
MVP
0.98
MPC
1.0
ClinPred
0.043
T
GERP RS
5.3
Varity_R
0.24
gMVP
0.59

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs141572096; hg19: chr4-13543700; API