14-52006627-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_007361.4(NID2):c.3914G>C(p.Gly1305Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000799 in 1,613,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007361.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NID2 | ENST00000216286.10 | c.3914G>C | p.Gly1305Ala | missense_variant | Exon 20 of 22 | 1 | NM_007361.4 | ENSP00000216286.4 | ||
RTRAF | ENST00000261700.8 | c.*2111C>G | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_016039.3 | ENSP00000261700.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251402Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135878
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461524Hom.: 0 Cov.: 31 AF XY: 0.0000908 AC XY: 66AN XY: 727074
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3914G>C (p.G1305A) alteration is located in exon 20 (coding exon 20) of the NID2 gene. This alteration results from a G to C substitution at nucleotide position 3914, causing the glycine (G) at amino acid position 1305 to be replaced by an alanine (A). 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