1-61082809-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001134673.4(NFIA):ā€‹c.18T>Cā€‹(p.Cys6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000716 in 1,396,640 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: not found (cov: 28)
Exomes š‘“: 0.0000072 ( 0 hom. )

Consequence

NFIA
NM_001134673.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.39
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 1-61082809-T-C is Benign according to our data. Variant chr1-61082809-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2083104.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.39 with no splicing effect.
BS2
High AC in GnomAdExome4 at 10 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFIANM_001134673.4 linkuse as main transcriptc.18T>C p.Cys6= synonymous_variant 1/11 ENST00000403491.8 NP_001128145.1
NFIANM_001145512.2 linkuse as main transcriptc.153T>C p.Cys51= synonymous_variant 2/12 NP_001138984.1
NFIANM_005595.5 linkuse as main transcriptc.18T>C p.Cys6= synonymous_variant 1/10 NP_005586.1
NFIANM_001145511.2 linkuse as main transcriptc.3+5181T>C intron_variant NP_001138983.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFIAENST00000403491.8 linkuse as main transcriptc.18T>C p.Cys6= synonymous_variant 1/111 NM_001134673.4 ENSP00000384523 P1Q12857-1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD3 exomes
AF:
0.0000584
AC:
9
AN:
154158
Hom.:
0
AF XY:
0.0000246
AC XY:
2
AN XY:
81288
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000364
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:
0.00000716
AC:
10
AN:
1396640
Hom.:
0
Cov.:
39
AF XY:
0.00000435
AC XY:
3
AN XY:
689062
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000281
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:
0.00
GnomAD4 genome
Cov.:
28
Bravo
AF:
0.0000113

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 11, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
13
DANN
Benign
0.81

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: rs777375238; hg19: chr1-61548481; API