rs13189050

Variant names:

• chr5-113370814-T-C
• rs13189050
• NM_001085377.2:c.415+14154A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-113370814-T-C
• chr5-113370814-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001085377.2(MCC):​c.415+14154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,116 control chromosomes in the GnomAD database, including 3,027 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 0.19 (3027 hom., cov: 32)
• Consequence: MCC NM_001085377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 0 publications found

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]

ENSG00000232633 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCC	NM_001085377.2	c.415+14154A>G		intron_variant	Intron 2 of 18	ENST00000408903.7	NP_001078846.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCC	ENST00000408903.7	c.415+14154A>G		intron_variant	Intron 2 of 18	2	NM_001085377.2	ENSP00000386227.3
ENSG00000232633	ENST00000416046.3	n.247-29129T>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28883 AN: 151998 Hom.: 3025 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28894 AN: 152116 Hom.: 3027 Cov.: 32 AF XY: 0.186 AC XY: 13858 AN XY: 74352

African (AFR) AF: 0.126 AC: 5218 AN: 41492

American (AMR) AF: 0.155 AC: 2373 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3468

East Asian (EAS) AF: 0.0893 AC: 463 AN: 5184

South Asian (SAS) AF: 0.148 AC: 714 AN: 4820

European-Finnish (FIN) AF: 0.208 AC: 2199 AN: 10550

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16518 AN: 67988

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.226 Hom.: 2073

Bravo AF: 0.183

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13189050; hg19: chr5-112706511; COSMIC: COSV68730037;