11-59831479-TTA-T

Position:

• chr11-59831479-TTA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005142.3(CBLIF):​c.1192+197_1192+198del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 201,834 control chromosomes in the GnomAD database, including 1,895 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1792 hom., cov: 27)
  • Exomes 𝑓: 0.22 (103 hom.)
• Consequence: CBLIF NM_005142.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.898

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-59831479-TTA-T is Benign according to our data. Variant chr11-59831479-TTA-T is described in ClinVar as [Benign]. Clinvar id is 1273950.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBLIF	NM_005142.3	c.1192+197_1192+198del		intron_variant		ENST00000257248.3
CBLIF	XM_011544939.4	c.1150+197_1150+198del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBLIF	ENST00000257248.3	c.1192+197_1192+198del		intron_variant		1	NM_005142.3	P1
CBLIF	ENST00000525058.5	c.*1159+197_*1159+198del		intron_variant, NMD_transcript_variant		2
CBLIF	ENST00000533067.1			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17250 AN: 146450 Hom.: 1769 Cov.: 27

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0732

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.0518

Gnomad OTH AF: 0.0915

GnomAD4 exome AF: 0.222 AC: 12307 AN: 55332 Hom.: 103 AF XY: 0.221 AC XY: 7145 AN XY: 32366

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.214

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.248

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.220

Gnomad4 OTH exome AF: 0.228

GnomAD4 genome AF: 0.118 AC: 17312 AN: 146502 Hom.: 1792 Cov.: 27 AF XY: 0.118 AC XY: 8383 AN XY: 71306

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0532

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0518

Gnomad4 OTH AF: 0.0916

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs3973727; hg19: chr11-59598952;