chr6-31025529-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395414.1(MUC22):āc.98A>Cā(p.Lys33Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000221 in 1,358,470 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 (ā ).
Frequency
Consequence
NM_001395414.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC22 | NM_001395414.1 | c.98A>C | p.Lys33Thr | missense_variant | 2/4 | ENST00000561890.1 | NP_001382343.1 | |
MUC22 | NM_001318484.1 | c.107A>C | p.Lys36Thr | missense_variant | 3/5 | NP_001305413.1 | ||
MUC22 | NM_001198815.1 | c.98A>C | p.Lys33Thr | missense_variant | 3/5 | NP_001185744.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC22 | ENST00000561890.1 | c.98A>C | p.Lys33Thr | missense_variant | 2/4 | 2 | NM_001395414.1 | ENSP00000455906 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000971 AC: 1AN: 103008Hom.: 0 AF XY: 0.0000178 AC XY: 1AN XY: 56110
GnomAD4 exome AF: 0.00000221 AC: 3AN: 1358470Hom.: 0 Cov.: 33 AF XY: 0.00000299 AC XY: 2AN XY: 669088
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2022 | The c.98A>C (p.K33T) alteration is located in exon 3 (coding exon 2) of the MUC22 gene. This alteration results from a A to C substitution at nucleotide position 98, causing the lysine (K) at amino acid position 33 to be replaced by a threonine (T). 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