10-87228352-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001099338.2(NUTM2A):c.472G>A(p.Gly158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099338.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152096Hom.: 1 Cov.: 21
GnomAD3 exomes AF: 0.000359 AC: 83AN: 231424Hom.: 0 AF XY: 0.000315 AC XY: 40AN XY: 127028
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000531 AC: 775AN: 1458518Hom.: 10 Cov.: 32 AF XY: 0.000518 AC XY: 376AN XY: 725568
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000368 AC: 56AN: 152212Hom.: 1 Cov.: 21 AF XY: 0.000363 AC XY: 27AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.472G>A (p.G158S) alteration is located in exon 2 (coding exon 2) of the NUTM2A gene. This alteration results from a G to A substitution at nucleotide position 472, causing the glycine (G) at amino acid position 158 to be replaced by a serine (S). 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