7-101032610-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040105.2(MUC17):c.1194G>A(p.Met398Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040105.2 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 |
---|---|---|---|---|---|---|---|
MUC17 | NM_001040105.2 | c.1194G>A | p.Met398Ile | missense_variant | 3/13 | ENST00000306151.9 | |
MUC17 | NR_133665.2 | n.1249G>A | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC17 | ENST00000306151.9 | c.1194G>A | p.Met398Ile | missense_variant | 3/13 | 1 | NM_001040105.2 | P1 | |
MUC17 | ENST00000379439.3 | c.1194G>A | p.Met398Ile | missense_variant, NMD_transcript_variant | 3/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151974Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251322Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135832
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461768Hom.: 0 Cov.: 34 AF XY: 0.0000495 AC XY: 36AN XY: 727176
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151974Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | The c.1194G>A (p.M398I) alteration is located in exon 3 (coding exon 3) of the MUC17 gene. This alteration results from a G to A substitution at nucleotide position 1194, causing the methionine (M) at amino acid position 398 to be replaced by an isoleucine (I). 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