Variant 11-59831479-TTATATATA-TTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBLIF	NM_005142.3 link	c.1192+193_1192+198delTATATA		intron_variant	Intron 8 of 8	ENST00000257248.3	NP_005133.2	P27352-1
CBLIF	XM_011544939.4 link	c.1150+193_1150+198delTATATA		intron_variant	Intron 8 of 8		XP_011543241.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CBLIF	ENST00000257248.3 link	c.1192+193_1192+198delTATATA	intron_variant	Intron 8 of 8	1	NM_005142.3	ENSP00000257248.2	P27352-1
CBLIF	ENST00000525058.5 link	n.1159+193_1159+198delTATATA	intron_variant	Intron 8 of 8	2		ENSP00000433196.1	E9PM21
CBLIF	ENST00000533067.1 link	n.46_51delTATATA	downstream_gene_variant		3

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

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.0217

Gnomad4 ASJ exome

AF:

0.000622

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00194

Gnomad4 FIN exome

AF:

0.00106

Gnomad4 NFE exome

AF:

0.000819

Gnomad4 OTH exome

AF:

0.0213

GnomAD4 genome

AF:

0.0185

AC:

2716

AN:

146864

Hom.:

Cov.:

AF XY:

0.0177

AC XY:

1268

AN XY:

71510

show subpopulations

Gnomad4 AFR

AF:

0.0619

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.000293

Gnomad4 EAS

AF:

0.000199

Gnomad4 SAS

AF:

0.000216

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000332

Gnomad4 OTH

AF:

0.0138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over