rs3825253

Variant names:

• chr12-108715505-A-G
• rs3825253
• NM_014325.4:c.-5-14182T>C

Variant summary

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

The NM_014325.4(CORO1C):​c.-5-14182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 152,024 control chromosomes in the GnomAD database, including 508 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 0.057 (508 hom., cov: 31)
• Consequence: CORO1C NM_014325.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 5 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CORO1C	NM_014325.4	c.-5-14182T>C		intron_variant	Intron 1 of 10	ENST00000261401.8	NP_055140.1
CORO1C	NM_001276471.2	c.-5-14182T>C		intron_variant	Intron 1 of 10		NP_001263400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO1C	ENST00000261401.8	c.-5-14182T>C		intron_variant	Intron 1 of 10	1	NM_014325.4	ENSP00000261401.3

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8656 AN: 151906 Hom.: 508 Cov.: 31

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0449

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0801

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0783

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

GnomAD4 genome AF: 0.0569 AC: 8652 AN: 152024 Hom.: 508 Cov.: 31 AF XY: 0.0555 AC XY: 4123 AN XY: 74302

African (AFR) AF: 0.0146 AC: 607 AN: 41468

American (AMR) AF: 0.0705 AC: 1077 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 336 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1624 AN: 5154

South Asian (SAS) AF: 0.0447 AC: 215 AN: 4808

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10592

Middle Eastern (MID) AF: 0.0793 AC: 23 AN: 290

European-Non Finnish (NFE) AF: 0.0641 AC: 4358 AN: 67954

Other (OTH) AF: 0.0784 AC: 166 AN: 2116

Alfa AF: 0.0620 Hom.: 199

Bravo AF: 0.0639

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.83
PhyloP100		-0.54
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: rs3825253; hg19: chr12-109109281;