chr1-61082806-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001134673.4(NFIA):c.15C>T(p.Leu5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,397,492 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 (★).
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
NFIA
NM_001134673.4 synonymous
NM_001134673.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.62
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 1-61082806-C-T is Benign according to our data. Variant chr1-61082806-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2820503.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.62 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFIA | NM_001134673.4 | c.15C>T | p.Leu5= | synonymous_variant | 1/11 | ENST00000403491.8 | NP_001128145.1 | |
NFIA | NM_001145512.2 | c.150C>T | p.Leu50= | synonymous_variant | 2/12 | NP_001138984.1 | ||
NFIA | NM_005595.5 | c.15C>T | p.Leu5= | synonymous_variant | 1/10 | NP_005586.1 | ||
NFIA | NM_001145511.2 | c.3+5178C>T | intron_variant | NP_001138983.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFIA | ENST00000403491.8 | c.15C>T | p.Leu5= | synonymous_variant | 1/11 | 1 | NM_001134673.4 | ENSP00000384523 | P1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
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28
GnomAD4 exome AF: 7.16e-7 AC: 1AN: 1397492Hom.: 0 Cov.: 40 AF XY: 0.00000145 AC XY: 1AN XY: 689492
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GnomAD4 genome Cov.: 28
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28
Bravo
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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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 06, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at