19-13024520-G-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365902.3(NFIX):c.28-501G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,515,198 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 19 hom. )
Consequence
NFIX
NM_001365902.3 intron
NM_001365902.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.450
Genes affected
NFIX (HGNC:7788): (nuclear factor I X) The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 19-13024520-G-C is Benign according to our data. Variant chr19-13024520-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1675724.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 280 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFIX | NM_001365902.3 | c.28-501G>C | intron_variant | ENST00000592199.6 | NP_001352831.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFIX | ENST00000592199.6 | c.28-501G>C | intron_variant | 5 | NM_001365902.3 | ENSP00000467512.1 |
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 281AN: 152224Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00328 AC: 4470AN: 1362856Hom.: 19 Cov.: 32 AF XY: 0.00341 AC XY: 2284AN XY: 669320
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GnomAD4 genome AF: 0.00184 AC: 280AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00156 AC XY: 116AN XY: 74506
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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 | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | NFIX: BS1 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at