rs1838544

Variant names:

• chr15-68521626-T-C
• rs1838544
• NM_001324014.1:c.-66+3033T>C

Variant summary

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

The NM_001324014.1(CORO2B):​c.-66+3033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,244 control chromosomes in the GnomAD database, including 1,594 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 0.13 (1594 hom., cov: 32)
• Consequence: CORO2B NM_001324014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 0 publications found

Genes affected

CORO2B (HGNC:2256): (coronin 2B) Enables talin binding activity and vinculin binding activity. Acts upstream of or within several processes, including negative regulation of cell-substrate adhesion; regulation of actin cytoskeleton organization; and regulation of establishment of protein localization. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324014.1. 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
	CORO2B	NM_001324014.1		c.-66+3033T>C		intron	N/A	NP_001310943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20123 AN: 152126 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.133 AC: 20175 AN: 152244 Hom.: 1594 Cov.: 32 AF XY: 0.128 AC XY: 9511 AN XY: 74456

African (AFR) AF: 0.208 AC: 8641 AN: 41528

American (AMR) AF: 0.103 AC: 1577 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0428 AC: 207 AN: 4832

European-Finnish (FIN) AF: 0.0842 AC: 893 AN: 10600

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7920 AN: 68020

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.116 Hom.: 570

Bravo AF: 0.137

Asia WGS AF: 0.0450 AC: 161 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.9
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1838544; hg19: chr15-68813965;