Variant rs2302264 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Variant links:

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]

CORO1B links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	c.1008-112C>T		intron_variant		ENST00000341356.10
CORO1B	NM_001018070.3 linkuse as main transcript	c.1008-112C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

57423

AN:

148770

Hom.:

11131

Cov.:

show subpopulations

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.:

AF XY:

0.422

AC XY:

255911

AN XY:

606828

show subpopulations

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.:

AF XY:

0.381

AC XY:

27688

AN XY:

72694

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over