11-59831479-TTATATATA-TTATATATATATATA

Variant names:

• chr11-59831479-T-TTATATA
• rs3973727
• NM_005142.3:c.1192+193_1192+198dupTATATA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005142.3(CBLIF):​c.1192+193_1192+198dupTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000066 in 60,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.000066 (0 hom.)
• Consequence: CBLIF NM_005142.3 intron
• Clinical Significance: Not reported in ClinVar
• 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBLIF	ENST00000257248.3	c.1192+198_1192+199insTATATA		intron_variant	Intron 8 of 8	1	NM_005142.3	ENSP00000257248.2
CBLIF	ENST00000525058.5	n.*1159+198_*1159+199insTATATA		intron_variant	Intron 8 of 8	2		ENSP00000433196.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.0000660 AC: 4 AN: 60642 Hom.: 0 AF XY: 0.0000562 AC XY: 2 AN XY: 35556

Gnomad4 AFR exome AF: 0.000509

Gnomad4 AMR exome AF: 0.000402

Gnomad4 ASJ exome AF: 0.000622

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000388

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;