Variant chr5-113071088-G-GCCTTGCGCTGTCTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001085377.2(MCC):c.1925+5_1925+6insAAGACAGCGCAAGG variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,458,726 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: not found (cov: 0)

Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

MCC
NM_001085377.2 splice_donor_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]

MCC links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MCC	NM_001085377.2 linkuse as main transcript	c.1925+5_1925+6insAAGACAGCGCAAGG		splice_donor_region_variant, intron_variant		ENST00000408903.7	NP_001078846.2
MCC	NM_002387.3 linkuse as main transcript	c.1355+5_1355+6insAAGACAGCGCAAGG		splice_donor_region_variant, intron_variant			NP_002378.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
MCC	ENST00000408903.7 linkuse as main transcript	c.1925+5_1925+6insAAGACAGCGCAAGG	splice_donor_region_variant, intron_variant	2	NM_001085377.2	ENSP00000386227	P1	P23508-2
MCC	ENST00000302475.9 linkuse as main transcript	c.1355+5_1355+6insAAGACAGCGCAAGG	splice_donor_region_variant, intron_variant	1		ENSP00000305617		P23508-1
MCC	ENST00000514701.5 linkuse as main transcript	c.1355+5_1355+6insAAGACAGCGCAAGG	splice_donor_region_variant, intron_variant	2		ENSP00000485220
MCC	ENST00000515367.6 linkuse as main transcript	c.1166+5_1166+6insAAGACAGCGCAAGG	splice_donor_region_variant, intron_variant	5		ENSP00000421615

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000130

AC:

AN:

1458726

Hom.:

Cov.:

AF XY:

0.0000124

AC XY:

AN XY:

725518

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000117

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000135

Gnomad4 OTH exome

AF:

0.0000498

GnomAD4 genome

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over