chr11-67439955-G-A

Variant names:

• chr11-67439955-G-A
• rs2302264
• NM_020441.3:c.1008-112C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020441.3. 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
	CORO1B	NM_020441.3	MANE Select	c.1008-112C>T		intron	N/A	NP_065174.1
	CORO1B	NM_001018070.3		c.1008-112C>T		intron	N/A	NP_001018080.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1B	ENST00000341356.10	TSL:1 MANE Select	c.1008-112C>T		intron	N/A	ENSP00000340211.5
	CORO1B	ENST00000393893.5	TSL:5	c.1008-112C>T		intron	N/A	ENSP00000377471.1
	CORO1B	ENST00000537042.5	TSL:5	n.*294-112C>T		intron	N/A	ENSP00000445330.1

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

African (AFR) AF: 0.338 AC: 9470 AN: 28048

American (AMR) AF: 0.563 AC: 19159 AN: 34034

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 6534 AN: 18964

East Asian (EAS) AF: 0.349 AC: 11357 AN: 32526

South Asian (SAS) AF: 0.267 AC: 19047 AN: 71450

European-Finnish (FIN) AF: 0.411 AC: 14138 AN: 34366

Middle Eastern (MID) AF: 0.382 AC: 1387 AN: 3634

European-Non Finnish (NFE) AF: 0.443 AC: 423965 AN: 957826

Other (OTH) AF: 0.416 AC: 21113 AN: 50718

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

African (AFR) AF: 0.319 AC: 13002 AN: 40744

American (AMR) AF: 0.450 AC: 6786 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1099 AN: 3430

East Asian (EAS) AF: 0.312 AC: 1479 AN: 4740

South Asian (SAS) AF: 0.272 AC: 1189 AN: 4366

European-Finnish (FIN) AF: 0.388 AC: 3911 AN: 10078

Middle Eastern (MID) AF: 0.283 AC: 82 AN: 290

European-Non Finnish (NFE) AF: 0.429 AC: 28824 AN: 67180

Other (OTH) AF: 0.371 AC: 774 AN: 2084

Alfa AF: 0.398 Hom.: 20948

Bravo AF: 0.389

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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