rs74440730

chr10-16878893-A-Cchr10-16878893-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001081.4(CUBN):c.8906-1796T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 152,268 control chromosomes in the GnomAD database, including 618 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.087 (618 hom., cov: 33)
• Consequence: CUBN NM_001081.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236

Genes affected

CUBN (HGNC:2548): (cubilin) Cubilin (CUBN) acts as a receptor for intrinsic factor-vitamin B12 complexes. The role of receptor is supported by the presence of 27 CUB domains. Cubulin is located within the epithelium of intestine and kidney. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUBN	NM_001081.4	c.8906-1796T>G		intron_variant		ENST00000377833.10
CUBN	XM_011519709.3	c.4892-1796T>G		intron_variant
CUBN	XM_011519710.3	c.4868-1796T>G		intron_variant
CUBN	XM_011519711.4	c.4748-1796T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUBN	ENST00000377833.10	c.8906-1796T>G		intron_variant		1	NM_001081.4	P1

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13262 AN: 152150 Hom.: 618 Cov.: 33

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0785

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0985

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0870 AC: 13252 AN: 152268 Hom.: 618 Cov.: 33 AF XY: 0.0848 AC XY: 6313 AN XY: 74462

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0785

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0887 Hom.: 100

Bravo AF: 0.0849

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.9
Dann	Benign	0.46

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: rs74440730; hg19: chr10-16920892;