11-59842516-GTTC-GTTCTTC

Variant names:

• chr11-59842516-G-GTTC
• rs770530971
• NM_005142.3:c.435_437dupGAA

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PM4_Supporting

The NM_005142.3(CBLIF):​c.435_437dupGAA​(p.Lys145dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. N146N) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CBLIF NM_005142.3 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 0 publications found

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: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_005142.3. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBLIF	NM_005142.3	c.435_437dupGAA	p.Lys145dup	disruptive_inframe_insertion	Exon 4 of 9	ENST00000257248.3	NP_005133.2
CBLIF	XM_011544939.4	c.435_437dupGAA	p.Lys145dup	disruptive_inframe_insertion	Exon 4 of 9		XP_011543241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBLIF	ENST00000257248.3	c.435_437dupGAA	p.Lys145dup	disruptive_inframe_insertion	Exon 4 of 9	1	NM_005142.3	ENSP00000257248.2
CBLIF	ENST00000525058.5	n.*402_*404dupGAA		non_coding_transcript_exon_variant	Exon 4 of 9	2		ENSP00000433196.1
CBLIF	ENST00000532070.1	n.925_927dupGAA		non_coding_transcript_exon_variant	Exon 3 of 3	2
CBLIF	ENST00000525058.5	n.*402_*404dupGAA		3_prime_UTR_variant	Exon 4 of 9	2		ENSP00000433196.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs770530971; hg19: chr11-59609989;