chr7-101032536-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040105.2(MUC17):c.1120C>T(p.Leu374Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00031 in 1,613,652 control chromosomes in the GnomAD database, including 1 homozygotes. 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.1120C>T | p.Leu374Phe | missense_variant | 3/13 | ENST00000306151.9 | |
MUC17 | NR_133665.2 | n.1175C>T | non_coding_transcript_exon_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC17 | ENST00000306151.9 | c.1120C>T | p.Leu374Phe | missense_variant | 3/13 | 1 | NM_001040105.2 | P1 | |
MUC17 | ENST00000379439.3 | c.1120C>T | p.Leu374Phe | missense_variant, NMD_transcript_variant | 3/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 151802Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000498 AC: 125AN: 251236Hom.: 1 AF XY: 0.000479 AC XY: 65AN XY: 135754
GnomAD4 exome AF: 0.000318 AC: 465AN: 1461850Hom.: 1 Cov.: 34 AF XY: 0.000331 AC XY: 241AN XY: 727220
GnomAD4 genome AF: 0.000237 AC: 36AN: 151802Hom.: 0 Cov.: 33 AF XY: 0.000283 AC XY: 21AN XY: 74142
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.1120C>T (p.L374F) alteration is located in exon 3 (coding exon 3) of the MUC17 gene. This alteration results from a C to T substitution at nucleotide position 1120, causing the leucine (L) at amino acid position 374 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