chr11-60334935-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139249.4(MS4A6E):c.40C>T(p.Leu14Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.40C>T | p.Leu14Phe | missense_variant | 2/5 | ENST00000684409.1 | |
MS4A6E | NR_170614.1 | n.208C>T | non_coding_transcript_exon_variant | 2/6 | |||
MS4A6E | NR_170615.1 | n.208C>T | non_coding_transcript_exon_variant | 2/5 | |||
MS4A6E | NR_170616.1 | n.208C>T | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6E | ENST00000684409.1 | c.40C>T | p.Leu14Phe | missense_variant | 2/5 | NM_139249.4 | P1 | ||
MS4A6E | ENST00000300182.8 | c.40C>T | p.Leu14Phe | missense_variant | 1/4 | 1 | P1 | ||
MS4A6E | ENST00000530509.1 | upstream_gene_variant | 3 | ||||||
MS4A6E | ENST00000532756.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251466Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135904
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461816Hom.: 0 Cov.: 37 AF XY: 0.0000220 AC XY: 16AN XY: 727214
GnomAD4 genome AF: 0.000236 AC: 36AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | The c.40C>T (p.L14F) alteration is located in exon 1 (coding exon 1) of the MS4A6E gene. This alteration results from a C to T substitution at nucleotide position 40, causing the leucine (L) at amino acid position 14 to be replaced by a phenylalanine (F). 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