1-212433056-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013349.5(NENF):c.113C>A(p.Ala38Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,191,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013349.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NENF | NM_013349.5 | c.113C>A | p.Ala38Asp | missense_variant | Exon 1 of 4 | ENST00000366988.5 | NP_037481.1 | |
NENF | NR_026598.2 | n.137C>A | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||
LOC105372906 | XR_922577.4 | n.-239G>T | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NENF | ENST00000366988.5 | c.113C>A | p.Ala38Asp | missense_variant | Exon 1 of 4 | 1 | NM_013349.5 | ENSP00000355955.3 | ||
NENF | ENST00000472389.1 | n.66C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
NENF | ENST00000473900.1 | n.84C>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 | |||||
NENF | ENST00000479589.5 | n.134C>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151420Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000279 AC: 29AN: 1040314Hom.: 0 Cov.: 30 AF XY: 0.0000285 AC XY: 14AN XY: 490598
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151528Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74064
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.113C>A (p.A38D) alteration is located in exon 1 (coding exon 1) of the NENF gene. This alteration results from a C to A substitution at nucleotide position 113, causing the alanine (A) at amino acid position 38 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at