chr11-67438507-G-A

Variant names:

• chr11-67438507-G-A
• rs872375
• NM_020441.3:c.1345-6C>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.1345-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,603,860 control chromosomes in the GnomAD database, including 136,491 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (11076 hom., cov: 35)
  • Exomes 𝑓: 0.41 (125415 hom.)
• Consequence: CORO1B NM_020441.3 splice_region, intron
• Scores: Splicing: ADA: 0.0001010
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 13 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1B	NM_020441.3	MANE Select	c.1345-6C>T		splice_region intron	N/A	NP_065174.1	Q9BR76
	CORO1B	NM_001018070.3		c.1345-6C>T		splice_region intron	N/A	NP_001018080.1	Q9BR76

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CORO1B	ENST00000341356.10	TSL:1 MANE Select	c.1345-6C>T		splice_region intron	N/A	ENSP00000340211.5	Q9BR76
	CORO1B	ENST00000955904.1		c.1384-6C>T		splice_region intron	N/A	ENSP00000625963.1
	CORO1B	ENST00000393893.5	TSL:5	c.1345-6C>T		splice_region intron	N/A	ENSP00000377471.1	Q9BR76

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57264 AN: 152130 Hom.: 11064 Cov.: 35

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.369

GnomAD2 exomes AF: 0.391 AC: 92911 AN: 237730 AF XY: 0.381

Gnomad AFR exome AF: 0.317

Gnomad AMR exome AF: 0.563

Gnomad ASJ exome AF: 0.315

Gnomad EAS exome AF: 0.286

Gnomad FIN exome AF: 0.353

Gnomad NFE exome AF: 0.416

Gnomad OTH exome AF: 0.391

GnomAD4 exome AF: 0.411 AC: 596934 AN: 1451612 Hom.: 125415 Cov.: 52 AF XY: 0.405 AC XY: 292122 AN XY: 720520

African (AFR) AF: 0.321 AC: 10694 AN: 33332

American (AMR) AF: 0.551 AC: 24398 AN: 44280

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 8036 AN: 25842

East Asian (EAS) AF: 0.307 AC: 12120 AN: 39440

South Asian (SAS) AF: 0.265 AC: 22750 AN: 85690

European-Finnish (FIN) AF: 0.357 AC: 18500 AN: 51774

Middle Eastern (MID) AF: 0.357 AC: 2050 AN: 5744

European-Non Finnish (NFE) AF: 0.429 AC: 474827 AN: 1105626

Other (OTH) AF: 0.393 AC: 23559 AN: 59884

GnomAD4 genome AF: 0.376 AC: 57313 AN: 152248 Hom.: 11076 Cov.: 35 AF XY: 0.370 AC XY: 27556 AN XY: 74462

African (AFR) AF: 0.314 AC: 13059 AN: 41552

American (AMR) AF: 0.445 AC: 6802 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1523 AN: 5188

South Asian (SAS) AF: 0.247 AC: 1195 AN: 4834

European-Finnish (FIN) AF: 0.352 AC: 3732 AN: 10612

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28714 AN: 67972

Other (OTH) AF: 0.367 AC: 775 AN: 2114

Alfa AF: 0.398 Hom.: 5273

Bravo AF: 0.388

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	-0.77
CADD	Benign	7.2
DANN	Benign	0.76
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00010
dbscSNV1_RF	Benign	0.016
SpliceAI score (max)		0.020		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: rs872375; hg19: chr11-67205978; COSMIC: COSV57047449; COSMIC: COSV57047449;