rs2274870
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015469.3(NIPSNAP3A):c.299G>A(p.Arg100Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 1,611,216 control chromosomes in the GnomAD database, including 318,828 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015469.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPSNAP3A | NM_015469.3 | c.299G>A | p.Arg100Gln | missense_variant | 3/6 | ENST00000374767.5 | |
NIPSNAP3A | NM_001329570.2 | c.299G>A | p.Arg100Gln | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPSNAP3A | ENST00000374767.5 | c.299G>A | p.Arg100Gln | missense_variant | 3/6 | 1 | NM_015469.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.654 AC: 99323AN: 151814Hom.: 33002 Cov.: 32
GnomAD3 exomes AF: 0.621 AC: 155963AN: 251176Hom.: 49151 AF XY: 0.616 AC XY: 83634AN XY: 135776
GnomAD4 exome AF: 0.624 AC: 910249AN: 1459284Hom.: 285785 Cov.: 38 AF XY: 0.622 AC XY: 451959AN XY: 726060
GnomAD4 genome ? AF: 0.654 AC: 99418AN: 151932Hom.: 33043 Cov.: 32 AF XY: 0.648 AC XY: 48109AN XY: 74210
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at