chr12-108697313-T-C

Variant names:

• chr12-108697313-T-C
• rs10746129
• NM_014325.4:c.195+3811A>G

Variant summary

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

The NM_001105237.2(CORO1C):​c.354+3811A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,938 control chromosomes in the GnomAD database, including 18,604 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 0.49 (18604 hom., cov: 31)
• Consequence: CORO1C NM_001105237.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 11 publications found

Genes affected

CORO1C (HGNC:2254): (coronin 1C) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105237.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1C	NM_014325.4	MANE Select	c.195+3811A>G		intron	N/A	NP_055140.1
	CORO1C	NM_001105237.2		c.354+3811A>G		intron	N/A	NP_001098707.1
	CORO1C	NM_001276471.2		c.195+3811A>G		intron	N/A	NP_001263400.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1C	ENST00000261401.8	TSL:1 MANE Select	c.195+3811A>G		intron	N/A	ENSP00000261401.3
	CORO1C	ENST00000420959.6	TSL:1	c.354+3811A>G		intron	N/A	ENSP00000394496.2
	CORO1C	ENST00000549772.5	TSL:1	c.213+3811A>G		intron	N/A	ENSP00000447534.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74317 AN: 151820 Hom.: 18581 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.490 AC: 74384 AN: 151938 Hom.: 18604 Cov.: 31 AF XY: 0.499 AC XY: 37079 AN XY: 74236

African (AFR) AF: 0.461 AC: 19084 AN: 41404

American (AMR) AF: 0.570 AC: 8715 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3496 AN: 5170

South Asian (SAS) AF: 0.695 AC: 3343 AN: 4812

European-Finnish (FIN) AF: 0.545 AC: 5745 AN: 10538

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30639 AN: 67952

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.467 Hom.: 53339

Bravo AF: 0.488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.9
DANN	Benign	0.82
PhyloP100		-0.68
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: rs10746129; hg19: chr12-109091089;