chr1-61082052-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001145512.2(NFIA):c.104+5G>C variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,546,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145512.2 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFIA | NM_001145511.2 | c.3+4424G>C | intron_variant | NP_001138983.1 | ||||
NFIA | NM_001145512.2 | c.104+5G>C | splice_donor_5th_base_variant, intron_variant | NP_001138984.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFIA | ENST00000371189.8 | c.104+5G>C | splice_donor_5th_base_variant, intron_variant | 2 | ENSP00000360231 | |||||
NFIA | ENST00000371191.5 | c.97-6097G>C | intron_variant | 5 | ENSP00000360233 | |||||
NFIA | ENST00000407417.7 | c.3+4424G>C | intron_variant | 2 | ENSP00000384680 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152064Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1394870Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 688172
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152064Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
Chromosome 1p32-p31 deletion syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Apr 05, 2020 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at