chr12-108667330-G-T

Variant names:

• chr12-108667330-G-T
• rs750134
• NM_014325.4:c.319-5172C>A

Variant summary

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

The NM_014325.4(CORO1C):​c.319-5172C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0714 in 152,210 control chromosomes in the GnomAD database, including 611 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 0.071 (611 hom., cov: 32)
• Consequence: CORO1C NM_014325.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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.319-5172C>A		intron	N/A	NP_055140.1
	CORO1C	NM_001105237.2		c.478-5172C>A		intron	N/A	NP_001098707.1
	CORO1C	NM_001276471.2		c.319-5172C>A		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.319-5172C>A		intron	N/A	ENSP00000261401.3
	CORO1C	ENST00000420959.6	TSL:1	c.478-5172C>A		intron	N/A	ENSP00000394496.2
	CORO1C	ENST00000549772.5	TSL:1	c.337-5172C>A		intron	N/A	ENSP00000447534.1

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10853 AN: 152092 Hom.: 609 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.0714 AC: 10870 AN: 152210 Hom.: 611 Cov.: 32 AF XY: 0.0699 AC XY: 5199 AN XY: 74406

African (AFR) AF: 0.0439 AC: 1825 AN: 41526

American (AMR) AF: 0.0768 AC: 1175 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1631 AN: 5170

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4824

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10596

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5043 AN: 68006

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.0712 Hom.: 113

Bravo AF: 0.0789

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.39
PhyloP100		-0.24
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: rs750134; hg19: chr12-109061106;