2-168851280-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001039724.4(NOSTRIN):c.731G>A(p.Cys244Tyr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000905 in 1,613,782 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039724.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOSTRIN | NM_001039724.4 | c.731G>A | p.Cys244Tyr | missense_variant, splice_region_variant | 10/16 | ENST00000317647.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOSTRIN | ENST00000317647.12 | c.731G>A | p.Cys244Tyr | missense_variant, splice_region_variant | 10/16 | 1 | NM_001039724.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000149 AC: 37AN: 248540Hom.: 0 AF XY: 0.000200 AC XY: 27AN XY: 134808
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461506Hom.: 2 Cov.: 31 AF XY: 0.000136 AC XY: 99AN XY: 727004
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2024 | The c.902G>A (p.C301Y) alteration is located in exon 15 (coding exon 11) of the NOSTRIN gene. This alteration results from a G to A substitution at nucleotide position 902, causing the cysteine (C) at amino acid position 301 to be replaced by a tyrosine (Y). 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