chr9-91410299-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005384.3(NFIL3):c.436G>T(p.Ala146Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,214 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFIL3 | NM_005384.3 | c.436G>T | p.Ala146Ser | missense_variant | 2/2 | ENST00000297689.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFIL3 | ENST00000297689.4 | c.436G>T | p.Ala146Ser | missense_variant | 2/2 | 1 | NM_005384.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152206Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251430Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135906
GnomAD4 exome AF: 0.0000622 AC: 91AN: 1461890Hom.: 1 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727244
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152324Hom.: 1 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | The c.436G>T (p.A146S) alteration is located in exon 2 (coding exon 1) of the NFIL3 gene. This alteration results from a G to T substitution at nucleotide position 436, causing the alanine (A) at amino acid position 146 to be replaced by a serine (S). 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