12-108646093-T-C

Variant names:

• chr12-108646093-T-C
• rs2111211
• NM_014325.4:c.*1310A>G

Variant summary

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

The NM_014325.4(CORO1C):​c.*1310A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,100 control chromosomes in the GnomAD database, including 25,359 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 0.57 (25354 hom., cov: 32)
  • Exomes 𝑓: 0.52 (5 hom.)
• Consequence: CORO1C NM_014325.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.52
• Publications: 9 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]

LOC105369968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014325.4. 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.*1310A>G		3_prime_UTR	Exon 11 of 11	NP_055140.1
	CORO1C	NM_001105237.2		c.*1310A>G		3_prime_UTR	Exon 11 of 11	NP_001098707.1
	CORO1C	NM_001276471.2		c.*1310A>G		3_prime_UTR	Exon 11 of 11	NP_001263400.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1C	ENST00000261401.8	TSL:1 MANE Select	c.*1310A>G		3_prime_UTR	Exon 11 of 11	ENSP00000261401.3
	CORO1C	ENST00000420959.6	TSL:1	c.*1310A>G		3_prime_UTR	Exon 11 of 11	ENSP00000394496.2
	ENSG00000257221	ENST00000797927.1		n.261+9638T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86355 AN: 151940 Hom.: 25318 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.524 AC: 22 AN: 42 Hom.: 5 Cov.: 0 AF XY: 0.567 AC XY: 17 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 18 AN: 36

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.569 AC: 86447 AN: 152058 Hom.: 25354 Cov.: 32 AF XY: 0.577 AC XY: 42869 AN XY: 74334

African (AFR) AF: 0.528 AC: 21871 AN: 41460

American (AMR) AF: 0.652 AC: 9967 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5147 AN: 5186

South Asian (SAS) AF: 0.748 AC: 3606 AN: 4824

European-Finnish (FIN) AF: 0.572 AC: 6049 AN: 10566

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35766 AN: 67958

Other (OTH) AF: 0.588 AC: 1239 AN: 2106

Alfa AF: 0.537 Hom.: 26002

Bravo AF: 0.575

Asia WGS AF: 0.852 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.078
DANN	Benign	0.55
PhyloP100		-4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2111211; hg19: chr12-109039869; COSMIC: COSV54599194; COSMIC: COSV54599194;