rs4248154
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001395414.1(MUC22):c.5223C>T(p.His1741=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,535,300 control chromosomes in the GnomAD database, including 27,879 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2470 hom., cov: 31)
Exomes 𝑓: 0.18 ( 25409 hom. )
Consequence
MUC22
NM_001395414.1 synonymous
NM_001395414.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.51
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP7
?
Synonymous conserved (PhyloP=-1.51 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC22 | NM_001395414.1 | c.5223C>T | p.His1741= | synonymous_variant | 4/4 | ENST00000561890.1 | |
MUC22 | NM_001318484.1 | c.5232C>T | p.His1744= | synonymous_variant | 5/5 | ||
MUC22 | NM_001198815.1 | c.5223C>T | p.His1741= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC22 | ENST00000561890.1 | c.5223C>T | p.His1741= | synonymous_variant | 4/4 | 2 | NM_001395414.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.172 AC: 26139AN: 151816Hom.: 2461 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
26139
AN:
151816
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.200 AC: 25667AN: 128446Hom.: 2771 AF XY: 0.205 AC XY: 14442AN XY: 70334
GnomAD3 exomes
AF:
AC:
25667
AN:
128446
Hom.:
AF XY:
AC XY:
14442
AN XY:
70334
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.184 AC: 254769AN: 1383364Hom.: 25409 Cov.: 36 AF XY: 0.188 AC XY: 128160AN XY: 682582
GnomAD4 exome
AF:
AC:
254769
AN:
1383364
Hom.:
Cov.:
36
AF XY:
AC XY:
128160
AN XY:
682582
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.172 AC: 26157AN: 151936Hom.: 2470 Cov.: 31 AF XY: 0.176 AC XY: 13066AN XY: 74280
GnomAD4 genome
?
AF:
AC:
26157
AN:
151936
Hom.:
Cov.:
31
AF XY:
AC XY:
13066
AN XY:
74280
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
875
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at