NM_000139.5:c.476T>A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000139.5(MS4A2):c.476T>A(p.Ile159Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000139.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MS4A2 | ENST00000278888.8 | c.476T>A | p.Ile159Asn | missense_variant | Exon 5 of 7 | 1 | NM_000139.5 | ENSP00000278888.3 | ||
MS4A2 | ENST00000617306.1 | c.341T>A | p.Ile114Asn | missense_variant | Exon 4 of 6 | 1 | ENSP00000482594.1 | |||
MS4A2 | ENST00000440896.2 | n.578T>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251490Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.476T>A (p.I159N) alteration is located in exon 5 (coding exon 5) of the MS4A2 gene. This alteration results from a T to A substitution at nucleotide position 476, causing the isoleucine (I) at amino acid position 159 to be replaced by an asparagine (N). 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