chr11-60337918-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_139249.4(MS4A6E):āc.325G>Cā(p.Asp109His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_139249.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A6E | NM_139249.4 | c.325G>C | p.Asp109His | missense_variant | 3/5 | ENST00000684409.1 | |
MS4A6E | NR_170614.1 | n.493G>C | non_coding_transcript_exon_variant | 3/6 | |||
MS4A6E | NR_170616.1 | n.613G>C | non_coding_transcript_exon_variant | 4/6 | |||
MS4A6E | NR_170615.1 | n.541+72G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6E | ENST00000684409.1 | c.325G>C | p.Asp109His | missense_variant | 3/5 | NM_139249.4 | P1 | ||
MS4A6E | ENST00000300182.8 | c.325G>C | p.Asp109His | missense_variant | 2/4 | 1 | P1 | ||
MS4A6E | ENST00000532756.1 | c.250G>C | p.Asp84His | missense_variant, NMD_transcript_variant | 2/5 | 4 | |||
MS4A6E | ENST00000530509.1 | c.*112+72G>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.325G>C (p.D109H) alteration is located in exon 2 (coding exon 2) of the MS4A6E gene. This alteration results from a G to C substitution at nucleotide position 325, causing the aspartic acid (D) at amino acid position 109 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