chr11-60306104-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_148975.3(MS4A4A):c.551T>C(p.Leu184Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,610,882 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L184M) has been classified as Likely benign.
Frequency
Consequence
NM_148975.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A4A | NM_148975.3 | c.551T>C | p.Leu184Pro | missense_variant | 6/7 | ENST00000337908.5 | |
MS4A4A | NM_024021.4 | c.494T>C | p.Leu165Pro | missense_variant | 7/8 | ||
MS4A4A | NM_001243266.2 | c.392T>C | p.Leu131Pro | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A4A | ENST00000337908.5 | c.551T>C | p.Leu184Pro | missense_variant | 6/7 | 1 | NM_148975.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250674Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135488
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1458524Hom.: 0 Cov.: 28 AF XY: 0.0000193 AC XY: 14AN XY: 725850
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.551T>C (p.L184P) alteration is located in exon 6 (coding exon 6) of the MS4A4A gene. This alteration results from a T to C substitution at nucleotide position 551, causing the leucine (L) at amino acid position 184 to be replaced by a proline (P). 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