12-108646093-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO1C	NM_014325.4	c.*1310A>G		3_prime_UTR_variant	11/11	ENST00000261401.8
LOC105369968	XR_007063449.1	n.11710T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CORO1C	ENST00000261401.8	c.*1310A>G		3_prime_UTR_variant	11/11	1	NM_014325.4	P1
CORO1C	ENST00000420959.6	c.*1310A>G		3_prime_UTR_variant	11/11	1

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

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.588

Alfa AF: 0.532 Hom.: 19078

Bravo AF: 0.575

Asia WGS AF: 0.852 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.078
Dann	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs2111211; hg19: chr12-109039869; COSMIC: COSV54599194; COSMIC: COSV54599194;