chr6-31026269-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001395414.1(MUC22):c.838A>T(p.Ile280Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 113,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395414.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC22 | NM_001395414.1 | c.838A>T | p.Ile280Phe | missense_variant | 2/4 | ENST00000561890.1 | NP_001382343.1 | |
MUC22 | NM_001318484.1 | c.847A>T | p.Ile283Phe | missense_variant | 3/5 | NP_001305413.1 | ||
MUC22 | NM_001198815.1 | c.838A>T | p.Ile280Phe | missense_variant | 3/5 | NP_001185744.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC22 | ENST00000561890.1 | c.838A>T | p.Ile280Phe | missense_variant | 2/4 | 2 | NM_001395414.1 | ENSP00000455906 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000299 AC: 34AN: 113818Hom.: 0 Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000858 AC: 99AN: 1154410Hom.: 4 Cov.: 64 AF XY: 0.000114 AC XY: 65AN XY: 569078
GnomAD4 genome AF: 0.000298 AC: 34AN: 113924Hom.: 0 Cov.: 29 AF XY: 0.000271 AC XY: 15AN XY: 55252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.838A>T (p.I280F) alteration is located in exon 3 (coding exon 2) of the MUC22 gene. This alteration results from a A to T substitution at nucleotide position 838, causing the isoleucine (I) at amino acid position 280 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