Genetic Variant NM_020441.3:c.*385G>T (chr11-67437991-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79

Publications

19 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

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.*385G>T		3_prime_UTR	Exon 11 of 11	NP_065174.1	Q9BR76
	CORO1B	NM_001018070.3		c.*385G>T		3_prime_UTR	Exon 12 of 12	NP_001018080.1	Q9BR76

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CORO1B	ENST00000341356.10	TSL:1 MANE Select	c.*385G>T	3_prime_UTR	Exon 11 of 11	ENSP00000340211.5	Q9BR76
CORO1B	ENST00000616321.4	TSL:2	n.*1117G>T	non_coding_transcript_exon	Exon 11 of 11	ENSP00000479949.1	A0A087WW53
CORO1B	ENST00000616321.4	TSL:2	n.*1117G>T	3_prime_UTR	Exon 11 of 11	ENSP00000479949.1	A0A087WW53

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79539

AN:

152132

Hom.:

23328

Cov.:

show subpopulations

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.:

AF XY:

0.417

AC XY:

42251

AN XY:

101364

show subpopulations

African (AFR)

AF:

0.810

AC:

5116

AN:

6316

American (AMR)

AF:

0.542

AC:

3823

AN:

7048

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

2498

AN:

7872

East Asian (EAS)

AF:

0.316

AC:

5717

AN:

18110

South Asian (SAS)

AF:

0.256

AC:

735

AN:

2870

European-Finnish (FIN)

AF:

0.382

AC:

6014

AN:

15752

Middle Eastern (MID)

AF:

0.395

AC:

438

AN:

1110

European-Non Finnish (NFE)

AF:

0.423

AC:

54334

AN:

128348

Other (OTH)

AF:

0.441

AC:

6011

AN:

13618

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2219

4437

6656

8874

11093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

272

544

816

1088

1360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.523

AC:

79621

AN:

152250

Hom.:

23364

Cov.:

AF XY:

0.512

AC XY:

38083

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.809

AC:

33624

AN:

41552

American (AMR)

AF:

0.506

AC:

7744

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1118

AN:

3468

East Asian (EAS)

AF:

0.293

AC:

1522

AN:

5190

South Asian (SAS)

AF:

0.249

AC:

1203

AN:

4830

European-Finnish (FIN)

AF:

0.372

AC:

3938

AN:

10598

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.427

AC:

29049

AN:

67998

Other (OTH)

AF:

0.468

AC:

989

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1807

3614

5421

7228

9035

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.597

Hom.:

7729

Bravo

AF:

0.551

Asia WGS

AF:

0.347

AC:

1209

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.034

(source)

DANN

Benign

0.36

PhyloP100

-2.8

PromoterAI

0.18

Neutral

(source)

Mutation Taster

=298/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over