12-108662601-T-C

Variant names:

• chr12-108662601-T-C
• rs10861957
• NM_014325.4:c.319-443A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014325.4(CORO1C):​c.319-443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,908 control chromosomes in the GnomAD database, including 24,899 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 0.56 (24899 hom., cov: 32)
• Consequence: CORO1C NM_014325.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• 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 rank	MANE	Protein	UniProt
CORO1C	NM_014325.4	c.319-443A>G		intron_variant	Intron 3 of 10	ENST00000261401.8	NP_055140.1
CORO1C	NM_001105237.2	c.478-443A>G		intron_variant	Intron 3 of 10		NP_001098707.1
CORO1C	NM_001276471.2	c.319-443A>G		intron_variant	Intron 3 of 10		NP_001263400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CORO1C	ENST00000261401.8	c.319-443A>G		intron_variant	Intron 3 of 10	1	NM_014325.4	ENSP00000261401.3

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85425 AN: 151790 Hom.: 24867 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.563 AC: 85511 AN: 151908 Hom.: 24899 Cov.: 32 AF XY: 0.572 AC XY: 42438 AN XY: 74256

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.584

Alfa AF: 0.555 Hom.: 3934

Bravo AF: 0.568

Asia WGS AF: 0.850 AC: 2949 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.92

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: rs10861957; hg19: chr12-109056377;