chr10-16919996-A-C

Position:

chr10-16919996-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001081.4(CUBN):c.6788T>G(p.Phe2263Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,874 control chromosomes in the GnomAD database, including 473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 37 hom., cov: 32)

Exomes 𝑓: 0.011 ( 436 hom. )

Consequence

CUBN
NM_001081.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 7.80

Variant links:

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]

CUBN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0049438477).

BP6

Variant 10-16919996-A-C is Benign according to our data. Variant chr10-16919996-A-C is described in ClinVar as [Benign]. Clinvar id is 299434.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUBN	NM_001081.4 linkuse as main transcript	c.6788T>G	p.Phe2263Cys	missense_variant	44/67	ENST00000377833.10	NP_001072.2	O60494

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUBN	ENST00000377833.10 linkuse as main transcript	c.6788T>G	p.Phe2263Cys	missense_variant	44/67	1	NM_001081.4	ENSP00000367064.4		O60494

Frequencies

GnomAD3 genomes

AF:

0.0108

AC:

1646

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.0451

Gnomad SAS

AF:

0.0806

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00501

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0172

AC:

4335

AN:

251342

Hom.:

159

AF XY:

0.0200

AC XY:

2712

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.0113

Gnomad AMR exome

AF:

0.00721

Gnomad ASJ exome

AF:

0.00605

Gnomad EAS exome

AF:

0.0418

Gnomad SAS exome

AF:

0.0780

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00526

Gnomad OTH exome

AF:

0.0134

GnomAD4 exome

AF:

0.0108

AC:

15758

AN:

1461552

Hom.:

436

Cov.:

AF XY:

0.0128

AC XY:

9315

AN XY:

727092

show subpopulations

Gnomad4 AFR exome

AF:

0.0121

Gnomad4 AMR exome

AF:

0.00740

Gnomad4 ASJ exome

AF:

0.00601

Gnomad4 EAS exome

AF:

0.0498

Gnomad4 SAS exome

AF:

0.0767

Gnomad4 FIN exome

AF:

0.000281

Gnomad4 NFE exome

AF:

0.00463

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0108

AC:

1645

AN:

152322

Hom.:

Cov.:

AF XY:

0.0122

AC XY:

911

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.0111

Gnomad4 AMR

AF:

0.0113

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.0453

Gnomad4 SAS

AF:

0.0798

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00501

Gnomad4 OTH

AF:

0.0133

Alfa

AF:

0.00695

Hom.:

Bravo

AF:

0.00994

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00597

AC:

ESP6500AA

AF:

0.0125

AC:

ESP6500EA

AF:

0.00442

AC:

ExAC

AF:

0.0184

AC:

2228

Asia WGS

AF:

0.0560

AC:

195

AN:

3478

EpiCase

AF:

0.00725

EpiControl

AF:

0.00747

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 02, 2023	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 22, 2019	This variant is associated with the following publications: (PMID: 30626930) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Imerslund-Grasbeck syndrome type 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 30, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Imerslund-Grasbeck syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.94

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.40

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.66

MetaRNN

Benign

0.0049

MetaSVM

Uncertain

-0.068

MutationAssessor

Pathogenic

4.6

PrimateAI

Uncertain

0.60

PROVEAN

Pathogenic

-7.3

REVEL

Uncertain

0.49

Sift

Uncertain

0.0020

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.36

MPC

0.53

ClinPred

0.061

GERP RS

5.1

Varity_R

0.55

gMVP

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over