chr11-60334954-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139249.4(MS4A6E):āc.59A>Gā(p.Asn20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,614,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A6E | NM_139249.4 | c.59A>G | p.Asn20Ser | missense_variant | 2/5 | ENST00000684409.1 | |
MS4A6E | NR_170614.1 | n.227A>G | non_coding_transcript_exon_variant | 2/6 | |||
MS4A6E | NR_170615.1 | n.227A>G | non_coding_transcript_exon_variant | 2/5 | |||
MS4A6E | NR_170616.1 | n.227A>G | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6E | ENST00000684409.1 | c.59A>G | p.Asn20Ser | missense_variant | 2/5 | NM_139249.4 | P1 | ||
MS4A6E | ENST00000300182.8 | c.59A>G | p.Asn20Ser | missense_variant | 1/4 | 1 | P1 | ||
MS4A6E | ENST00000530509.1 | upstream_gene_variant | 3 | ||||||
MS4A6E | ENST00000532756.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251476Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135916
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461862Hom.: 0 Cov.: 37 AF XY: 0.0000701 AC XY: 51AN XY: 727238
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.59A>G (p.N20S) alteration is located in exon 1 (coding exon 1) of the MS4A6E gene. This alteration results from a A to G substitution at nucleotide position 59, causing the asparagine (N) at amino acid position 20 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