rs3973727

Variant names:

• chr11-59831479-TTATATATA-T
• rs3973727
• NM_005142.3:c.1192+191_1192+198delTATATATA

Your query was ambiguous. Multiple possible variants found:

• chr11-59831479-TTATATATA-T
• chr11-59831479-TTATATATA-TTA
• chr11-59831479-TTATATATA-TTATA
• chr11-59831479-TTATATATA-TTATATA
• chr11-59831479-TTATATATA-TTATATATATA
• chr11-59831479-TTATATATA-TTATATATATATA
• chr11-59831479-TTATATATA-TTATATATATATATA

Variant summary

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

The NM_005142.3(CBLIF):​c.1192+191_1192+198delTATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 207,448 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: 𝑓 0.000027 (0 hom., cov: 27)
  • Exomes 𝑓: 0.000049 (0 hom.)
• Consequence: CBLIF NM_005142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

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+191_1192+198delTATATATA		intron_variant	Intron 8 of 8	ENST00000257248.3	NP_005133.2
CBLIF	XM_011544939.4	c.1150+191_1150+198delTATATATA		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+191_1192+198delTATATATA		intron_variant	Intron 8 of 8	1	NM_005142.3	ENSP00000257248.2
CBLIF	ENST00000525058.5	n.*1159+191_*1159+198delTATATATA		intron_variant	Intron 8 of 8	2		ENSP00000433196.1
CBLIF	ENST00000533067.1	n.*44_*51delTATATATA		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0000272 AC: 4 AN: 146816 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.0000990

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000495 AC: 3 AN: 60632 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 35550

Gnomad4 AFR exome AF: 0.00153

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000272 AC: 4 AN: 146816 Hom.: 0 Cov.: 27 AF XY: 0.0000280 AC XY: 2 AN XY: 71440

Gnomad4 AFR AF: 0.0000990

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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;