11-67437991-C-A

Position:

• chr11-67437991-C-A

Variant summary

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

The NM_020441.3(CORO1B):​c.*385G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 353,294 control chromosomes in the GnomAD database, including 42,242 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 0.52 (23364 hom., cov: 34)
  • Exomes 𝑓: 0.42 (18878 hom.)
• Consequence: CORO1B NM_020441.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CORO1B	NM_020441.3	c.*385G>T		3_prime_UTR_variant	11/11	ENST00000341356.10
CORO1B	NM_001018070.3	c.*385G>T		3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CORO1B	ENST00000341356.10	c.*385G>T		3_prime_UTR_variant	11/11	1	NM_020441.3	P1
CORO1B	ENST00000616321.4	c.*1117G>T		3_prime_UTR_variant, NMD_transcript_variant	11/11	2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79539 AN: 152132 Hom.: 23328 Cov.: 34

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.471

GnomAD4 exome AF: 0.421 AC: 84686 AN: 201044 Hom.: 18878 Cov.: 2 AF XY: 0.417 AC XY: 42251 AN XY: 101364

Gnomad4 AFR exome AF: 0.810

Gnomad4 AMR exome AF: 0.542

Gnomad4 ASJ exome AF: 0.317

Gnomad4 EAS exome AF: 0.316

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.382

Gnomad4 NFE exome AF: 0.423

Gnomad4 OTH exome AF: 0.441

GnomAD4 genome AF: 0.523 AC: 79621 AN: 152250 Hom.: 23364 Cov.: 34 AF XY: 0.512 AC XY: 38083 AN XY: 74440

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.468

Alfa AF: 0.488 Hom.: 3263

Bravo AF: 0.551

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.034
DANN	Benign	0.36

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: rs869736; hg19: chr11-67205462;