1-61081990-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate

The NM_001145512.2(NFIA):​c.47C>T​(p.Thr16Met) 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. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Consequence

NFIA
NM_001145512.2 missense

Scores

2
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.832
Variant links:
Genes affected
NFIA (HGNC:7784): (nuclear factor I A) This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), NFIA. . Gene score misZ 3.231 (greater than the threshold 3.09). Trascript score misZ 3.286 (greater than threshold 3.09). GenCC has associacion of gene with chromosome 1p32-p31 deletion syndrome, brain malformations with or without urinary tract defects.
BP4
Computational evidence support a benign effect (MetaRNN=0.1190297).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFIANM_001145512.2 linkuse as main transcriptc.47C>T p.Thr16Met missense_variant 1/12 NP_001138984.1
NFIANM_001145511.2 linkuse as main transcriptc.3+4362C>T intron_variant NP_001138983.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFIAENST00000371189.8 linkuse as main transcriptc.47C>T p.Thr16Met missense_variant 1/122 ENSP00000360231 Q12857-4
NFIAENST00000371191.5 linkuse as main transcriptc.97-6159C>T intron_variant 5 ENSP00000360233
NFIAENST00000407417.7 linkuse as main transcriptc.3+4362C>T intron_variant 2 ENSP00000384680 Q12857-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxDec 15, 2022Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Reported using an alternate transcript of the gene -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
16
DANN
Benign
0.95
Eigen
Benign
-0.46
Eigen_PC
Benign
-0.49
FATHMM_MKL
Benign
0.079
N
LIST_S2
Benign
0.52
T
M_CAP
Benign
0.039
D
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-0.25
N
REVEL
Benign
0.081
Sift
Benign
0.042
D
Sift4G
Uncertain
0.023
D
Vest4
0.30
MutPred
0.18
Loss of glycosylation at T16 (P = 0.0029);
MVP
0.18
MPC
0.86
ClinPred
0.27
T
GERP RS
2.7
gMVP
0.49

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-61547662; API