chr6-30986526-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001010909.5(MUC21):​c.351C>T​(p.Ala117Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,586,744 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00082 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000099 ( 3 hom. )

Consequence

MUC21
NM_001010909.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.46
Variant links:
Genes affected
MUC21 (HGNC:21661): (mucin 21, cell surface associated) This gene encodes a large membrane-bound glycoprotein which is a member of the mucin family. Mucins are O-glycosylated proteins that play an essential role in forming protective mucous barriers on epithelial surfaces. These proteins also play a role in intracellular signaling. The encoded protein contains an N-terminal signal sequence, an extracellular mucin domain, a stem domain, a transmembrane domain, and a C-terminal cytoplasmic tail domain. The mucin domain contains O-glycosylation sites and is polymorphic with isoforms containing a variable number of nonidentical proline-, threonine-, and serine-rich tandem repeats of 15 amino acids each. The aberrent expression of this gene is associated with lung adenocarcinoma. [provided by RefSeq, May 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 6-30986526-C-T is Benign according to our data. Variant chr6-30986526-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3898073.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.46 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MUC21NM_001010909.5 linkc.351C>T p.Ala117Ala synonymous_variant Exon 2 of 3 ENST00000376296.3 NP_001010909.2 Q5SSG8-1
MUC21NR_130720.3 linkn.734C>T non_coding_transcript_exon_variant Exon 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MUC21ENST00000376296.3 linkc.351C>T p.Ala117Ala synonymous_variant Exon 2 of 3 1 NM_001010909.5 ENSP00000365473.3 Q5SSG8-1
MUC21ENST00000486149 linkc.-1012C>T 5_prime_UTR_variant Exon 2 of 3 1 ENSP00000457640.1 A0A0C4DGM6

Frequencies

GnomAD3 genomes
AF:
0.000816
AC:
123
AN:
150774
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.00280
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000330
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000295
Gnomad OTH
AF:
0.000965
GnomAD3 exomes
AF:
0.000251
AC:
63
AN:
251282
Hom.:
0
AF XY:
0.000162
AC XY:
22
AN XY:
135826
show subpopulations
Gnomad AFR exome
AF:
0.00352
Gnomad AMR exome
AF:
0.0000868
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000989
AC:
142
AN:
1435856
Hom.:
3
Cov.:
168
AF XY:
0.0000644
AC XY:
46
AN XY:
713960
show subpopulations
Gnomad4 AFR exome
AF:
0.00388
Gnomad4 AMR exome
AF:
0.0000932
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000273
Gnomad4 OTH exome
AF:
0.000187
GnomAD4 genome
AF:
0.000822
AC:
124
AN:
150888
Hom.:
0
Cov.:
34
AF XY:
0.000813
AC XY:
60
AN XY:
73758
show subpopulations
Gnomad4 AFR
AF:
0.00282
Gnomad4 AMR
AF:
0.000330
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000295
Gnomad4 OTH
AF:
0.000955
Alfa
AF:
0.000560
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Apr 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

MUC21: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.3
DANN
Benign
0.44

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs532413302; hg19: chr6-30954303; COSMIC: COSV66220761; API