13-79481289-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019080.3(NDFIP2):c.86G>A(p.Gly29Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000937 in 1,387,152 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G29R) has been classified as Likely benign.
Frequency
Consequence
NM_019080.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDFIP2 | NM_019080.3 | c.86G>A | p.Gly29Glu | missense_variant | 1/8 | ENST00000218652.12 | |
NDFIP2 | NM_001394685.1 | c.86G>A | p.Gly29Glu | missense_variant | 1/8 | ||
NDFIP2 | NM_001161407.2 | c.86G>A | p.Gly29Glu | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDFIP2 | ENST00000218652.12 | c.86G>A | p.Gly29Glu | missense_variant | 1/8 | 1 | NM_019080.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000150 AC: 2AN: 133188Hom.: 0 AF XY: 0.0000275 AC XY: 2AN XY: 72734
GnomAD4 exome AF: 0.00000937 AC: 13AN: 1387152Hom.: 0 Cov.: 31 AF XY: 0.00000877 AC XY: 6AN XY: 684428
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2023 | The c.86G>A (p.G29E) alteration is located in exon 1 (coding exon 1) of the NDFIP2 gene. This alteration results from a G to A substitution at nucleotide position 86, causing the glycine (G) at amino acid position 29 to be replaced by a glutamic acid (E). 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