11-67439955-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020441.3(CORO1B):​c.1008-112C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000672 in 148,824 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000067 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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>A		intron	N/A	NP_065174.1
	CORO1B	NM_001018070.3		c.1008-112C>A		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>A		intron	N/A	ENSP00000340211.5
	CORO1B	ENST00000393893.5	TSL:5	c.1008-112C>A		intron	N/A	ENSP00000377471.1
	CORO1B	ENST00000537042.5	TSL:5	n.*294-112C>A		intron	N/A	ENSP00000445330.1

Frequencies

GnomAD3 genomes AF: 0.00000672 AC: 1 AN: 148824 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1233588 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 607794

African (AFR) AF: 0.00 AC: 0 AN: 28092

American (AMR) AF: 0.00 AC: 0 AN: 34068

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18980

East Asian (EAS) AF: 0.00 AC: 0 AN: 32546

South Asian (SAS) AF: 0.00 AC: 0 AN: 71500

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34400

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3640

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 959566

Other (OTH) AF: 0.00 AC: 0 AN: 50796

GnomAD4 genome AF: 0.00000672 AC: 1 AN: 148824 Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1 AN XY: 72606

African (AFR) AF: 0.00 AC: 0 AN: 40642

American (AMR) AF: 0.00 AC: 0 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3430

East Asian (EAS) AF: 0.00 AC: 0 AN: 4748

South Asian (SAS) AF: 0.00 AC: 0 AN: 4364

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10082

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.0000149 AC: 1 AN: 67200

Other (OTH) AF: 0.00 AC: 0 AN: 2062

Alfa AF: 0.00 Hom.: 20948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;