rs8017377
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025081.3(NYNRIN):c.2932G>A(p.Ala978Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 1,612,694 control chromosomes in the GnomAD database, including 156,619 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_025081.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NYNRIN | NM_025081.3 | c.2932G>A | p.Ala978Thr | missense_variant | 9/9 | ENST00000382554.4 | NP_079357.2 | |
NYNRIN | XM_011537016.2 | c.292G>A | p.Ala98Thr | missense_variant | 4/4 | XP_011535318.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NYNRIN | ENST00000382554.4 | c.2932G>A | p.Ala978Thr | missense_variant | 9/9 | 5 | NM_025081.3 | ENSP00000371994 | P1 | |
NYNRIN | ENST00000554505.1 | n.388G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.342 AC: 52017AN: 151932Hom.: 10581 Cov.: 32
GnomAD3 exomes AF: 0.366 AC: 90726AN: 247982Hom.: 19143 AF XY: 0.380 AC XY: 51029AN XY: 134328
GnomAD4 exome AF: 0.436 AC: 636622AN: 1460644Hom.: 146044 Cov.: 51 AF XY: 0.436 AC XY: 316871AN XY: 726554
GnomAD4 genome AF: 0.342 AC: 52019AN: 152050Hom.: 10575 Cov.: 32 AF XY: 0.337 AC XY: 25036AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at