rs11283943

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001085377.2(MCC):​c.1925+5_1925+6insAAGACAGTGCGAGG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,610,664 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00015 ( 0 hom. )

Consequence

MCC
NM_001085377.2 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14
Variant links:
Genes affected
MCC (HGNC:6935): (MCC regulator of WNT signaling pathway) This gene is a candidate colorectal tumor suppressor gene that is thought to negatively regulate cell cycle progression. The orthologous gene in the mouse expresses a phosphoprotein associated with the plasma membrane and membrane organelles, and overexpression of the mouse protein inhibits entry into S phase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MCCNM_001085377.2 linkc.1925+5_1925+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 12 of 18 ENST00000408903.7 NP_001078846.2 P23508-2
MCCNM_002387.3 linkc.1355+5_1355+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 10 of 16 NP_002378.2 P23508-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MCCENST00000408903.7 linkc.1925+5_1925+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 12 of 18 2 NM_001085377.2 ENSP00000386227.3 P23508-2
MCCENST00000302475.9 linkc.1355+5_1355+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 10 of 16 1 ENSP00000305617.4 P23508-1
MCCENST00000515367.6 linkc.1166+5_1166+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 10 of 16 5 ENSP00000421615.2 D6REY2
MCCENST00000514701.5 linkc.1355+5_1355+6insAAGACAGTGCGAGG splice_region_variant, intron_variant Intron 10 of 13 2 ENSP00000485220.1 A0A096LNU0

Frequencies

GnomAD3 genomes
AF:
0.000125
AC:
19
AN:
151824
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00367
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.000338
AC:
82
AN:
242414
AF XY:
0.000374
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00455
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000910
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000153
AC:
223
AN:
1458722
Hom.:
0
Cov.:
35
AF XY:
0.000160
AC XY:
116
AN XY:
725516
show subpopulations
Gnomad4 AFR exome
AF:
0.00
AC:
0
AN:
33362
Gnomad4 AMR exome
AF:
0.00
AC:
0
AN:
44442
Gnomad4 ASJ exome
AF:
0.00
AC:
0
AN:
26064
Gnomad4 EAS exome
AF:
0.00546
AC:
216
AN:
39592
Gnomad4 SAS exome
AF:
0.00
AC:
0
AN:
85572
Gnomad4 FIN exome
AF:
0.00
AC:
0
AN:
53334
Gnomad4 NFE exome
AF:
0.00000180
AC:
2
AN:
1110374
Gnomad4 Remaining exome
AF:
0.0000830
AC:
5
AN:
60260
Heterozygous variant carriers
0
10
20
29
39
49
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000125
AC:
19
AN:
151942
Hom.:
0
Cov.:
0
AF XY:
0.000148
AC XY:
11
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.00
AC:
0
AN:
0
Gnomad4 AMR
AF:
0.00
AC:
0
AN:
0
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00368
AC:
0.00367932
AN:
0.00367932
Gnomad4 SAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.00
AC:
0
AN:
0
Gnomad4 OTH
AF:
0.00
AC:
0
AN:
0
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0000398
Hom.:
1195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs11283943; hg19: chr5-112406785; API