Genetic Variant CBLIF:c.1192+193_1192+198delTATATA (chr11-59831479-TTATATA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005142.3(CBLIF):c.1192+193_1192+198delTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 207,472 control chromosomes in the GnomAD database, including 120 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.018 ( 76 hom., cov: 27)

Exomes 𝑓: 0.0084 ( 44 hom. )

Consequence

CBLIF
NM_005142.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.356

Publications

0 publications found

Variant links:

Genes affected

CBLIF (HGNC:4268): (cobalamin binding intrinsic factor) This gene is a member of the cobalamin transport protein family. It encodes a glycoprotein secreted by parietal cells of the gastric mucosa and is required for adequate absorption of vitamin B12. Vitamin B12 is necessary for erythrocyte maturation and mutations in this gene may lead to congenital pernicious anemia. [provided by RefSeq, Jul 2008]

CBLIF Gene-Disease associations (from GenCC):

hereditary intrinsic factor deficiency
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

CBLIF links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005142.3. 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
	CBLIF	NM_005142.3	MANE Select	c.1192+193_1192+198delTATATA		intron	N/A	NP_005133.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CBLIF	ENST00000257248.3	TSL:1 MANE Select	c.1192+193_1192+198delTATATA	intron	N/A	ENSP00000257248.2	P27352-1
CBLIF	ENST00000525058.5	TSL:2	n.1159+193_1159+198delTATATA	intron	N/A	ENSP00000433196.1	E9PM21
CBLIF	ENST00000533067.1	TSL:3	n.46_51delTATATA	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.0184

AC:

2706

AN:

146808

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0617

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.000293

Gnomad EAS

AF:

0.000198

Gnomad SAS

AF:

0.000430

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00321

Gnomad NFE

AF:

0.000332

Gnomad OTH

AF:

0.0139

GnomAD4 exome

AF:

0.00838

AC:

508

AN:

60608

Hom.:

AF XY:

0.00630

AC XY:

224

AN XY:

35540

show subpopulations

African (AFR)

AF:

0.171

AC:

334

AN:

1958

American (AMR)

AF:

0.0217

AC:

AN:

2488

Ashkenazi Jewish (ASJ)

AF:

0.000622

AC:

AN:

1608

East Asian (EAS)

AF:

0.00

AC:

AN:

3646

South Asian (SAS)

AF:

0.00194

AC:

AN:

2578

European-Finnish (FIN)

AF:

0.00106

AC:

AN:

1882

Middle Eastern (MID)

AF:

0.0119

AC:

AN:

252

European-Non Finnish (NFE)

AF:

0.000819

AC:

AN:

42716

Other (OTH)

AF:

0.0213

AC:

AN:

3480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.653

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0185

AC:

2716

AN:

146864

Hom.:

Cov.:

AF XY:

0.0177

AC XY:

1268

AN XY:

71510

show subpopulations

African (AFR)

AF:

0.0619

AC:

2506

AN:

40514

American (AMR)

AF:

0.0107

AC:

156

AN:

14578

Ashkenazi Jewish (ASJ)

AF:

0.000293

AC:

AN:

3410

East Asian (EAS)

AF:

0.000199

AC:

AN:

5036

South Asian (SAS)

AF:

0.000216

AC:

AN:

4638

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9202

Middle Eastern (MID)

AF:

0.00350

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.000332

AC:

AN:

66268

Other (OTH)

AF:

0.0138

AC:

AN:

2030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

122

244

366

488

610

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.36

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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11-59831479-TTATATATATATATATA-TTATATATATA

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