11-60337907-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_139249.4(MS4A6E):c.314C>T(p.Pro105Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,070 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 Likely benign (★).
Frequency
Consequence
NM_139249.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A6E | NM_139249.4 | c.314C>T | p.Pro105Leu | missense_variant | 3/5 | ENST00000684409.1 | |
MS4A6E | NR_170614.1 | n.482C>T | non_coding_transcript_exon_variant | 3/6 | |||
MS4A6E | NR_170616.1 | n.602C>T | non_coding_transcript_exon_variant | 4/6 | |||
MS4A6E | NR_170615.1 | n.541+61C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6E | ENST00000684409.1 | c.314C>T | p.Pro105Leu | missense_variant | 3/5 | NM_139249.4 | P1 | ||
MS4A6E | ENST00000300182.8 | c.314C>T | p.Pro105Leu | missense_variant | 2/4 | 1 | P1 | ||
MS4A6E | ENST00000532756.1 | c.239C>T | p.Pro80Leu | missense_variant, NMD_transcript_variant | 2/5 | 4 | |||
MS4A6E | ENST00000530509.1 | c.*112+61C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251304Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135798
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at