chr2-168861971-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039724.4(NOSTRIN):c.1306G>A(p.Ala436Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039724.4 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 |
---|---|---|---|---|---|---|---|
NOSTRIN | NM_001039724.4 | c.1306G>A | p.Ala436Thr | missense_variant | 15/16 | ENST00000317647.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOSTRIN | ENST00000317647.12 | c.1306G>A | p.Ala436Thr | missense_variant | 15/16 | 1 | NM_001039724.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249210Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135198
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461818Hom.: 0 Cov.: 30 AF XY: 0.0000770 AC XY: 56AN XY: 727202
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.1477G>A (p.A493T) alteration is located in exon 20 (coding exon 16) of the NOSTRIN gene. This alteration results from a G to A substitution at nucleotide position 1477, causing the alanine (A) at amino acid position 493 to be replaced by a threonine (T). 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