rs1838544

chr15-68521626-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CORO2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO2B	NM_001324014.1	c.-66+3033T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.135

Alfa AF: 0.115 Hom.: 509

Bravo AF: 0.137

Asia WGS AF: 0.0450 AC: 161 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	8.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1838544; hg19: chr15-68813965;