9-137449449-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001130969.3(NSMF):c.1538G>A(p.Arg513His) variant causes a missense change. The variant allele was found at a frequency of 0.0000657 in 1,612,784 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130969.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NSMF | ENST00000371475.9 | c.1538G>A | p.Arg513His | missense_variant | Exon 16 of 16 | 1 | NM_001130969.3 | ENSP00000360530.3 | ||
NSMF | ENST00000371472.6 | c.1532G>A | p.Arg511His | missense_variant | Exon 15 of 16 | 2 | ENSP00000360527.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250328Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135734
GnomAD4 exome AF: 0.0000692 AC: 101AN: 1460584Hom.: 0 Cov.: 31 AF XY: 0.0000702 AC XY: 51AN XY: 726596
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1532G>A (p.R511H) alteration is located in exon 15 (coding exon 15) of the NSMF gene. This alteration results from a G to A substitution at nucleotide position 1532, causing the arginine (R) at amino acid position 511 to be replaced by a histidine (H). 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