11-67439955-G-A

Position:

• chr11-67439955-G-A

Variant summary

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

The NM_020441.3(CORO1B):​c.1008-112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 1,380,470 control chromosomes in the GnomAD database, including 122,711 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 0.39 (11148 hom., cov: 31)
  • Exomes 𝑓: 0.43 (111563 hom.)
• Consequence: CORO1B NM_020441.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

Genes affected

CORO1B (HGNC:2253): (coronin 1B) Members of the coronin family, such as CORO1B, are WD repeat-containing actin-binding proteins that regulate cell motility (Cai et al., 2005 [PubMed 16027158]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO1B	NM_020441.3	c.1008-112C>T		intron_variant		ENST00000341356.10
CORO1B	NM_001018070.3	c.1008-112C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CORO1B	ENST00000341356.10	c.1008-112C>T		intron_variant		1	NM_020441.3	P1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 57423 AN: 148770 Hom.: 11131 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.427 AC: 526170 AN: 1231566 Hom.: 111563 Cov.: 19 AF XY: 0.422 AC XY: 255911 AN XY: 606828

Gnomad4 AFR exome AF: 0.338

Gnomad4 AMR exome AF: 0.563

Gnomad4 ASJ exome AF: 0.345

Gnomad4 EAS exome AF: 0.349

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.411

Gnomad4 NFE exome AF: 0.443

Gnomad4 OTH exome AF: 0.416

GnomAD4 genome AF: 0.386 AC: 57479 AN: 148904 Hom.: 11148 Cov.: 31 AF XY: 0.381 AC XY: 27688 AN XY: 72694

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.371

Alfa AF: 0.401 Hom.: 15688

Bravo AF: 0.389

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.59

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: rs2302264; hg19: chr11-67207426; COSMIC: COSV57049382; COSMIC: COSV57049382;