Variant rs2232785 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016579.4(CD320):c.502+118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 725,596 control chromosomes in the GnomAD database, including 3,257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 2037 hom., cov: 33)

Exomes 𝑓: 0.046 ( 1220 hom. )

Consequence

CD320
NM_016579.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

CD320 (HGNC:16692): (CD320 molecule) This gene encodes the transcobalamin receptor that is expressed at the cell surface. It mediates the cellular uptake of transcobalamin bound cobalamin (vitamin B12), and is involved in B-cell proliferation and immunoglobulin secretion. Mutations in this gene are associated with methylmalonic aciduria. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

CD320 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-8303737-C-T is Benign according to our data. Variant chr19-8303737-C-T is described in ClinVar as [Benign]. Clinvar id is 1292290.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD320	NM_016579.4 linkuse as main transcript	c.502+118G>A		intron_variant		ENST00000301458.10	NP_057663.1	Q9NPF0-1
CD320	NM_001165895.2 linkuse as main transcript	c.376+118G>A		intron_variant			NP_001159367.1	Q9NPF0-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CD320	ENST00000301458.10 linkuse as main transcript	c.502+118G>A	intron_variant	1	NM_016579.4	ENSP00000301458.4	Q9NPF0-1
CD320	ENST00000596002.5 linkuse as main transcript	n.*790+118G>A	intron_variant	1		ENSP00000471773.1	M0R1C4
CD320	ENST00000537716.6 linkuse as main transcript	c.376+118G>A	intron_variant	2		ENSP00000437697.1	Q9NPF0-2
CD320	ENST00000599573.1 linkuse as main transcript	n.*102+118G>A	intron_variant	2		ENSP00000471551.1	M0R100

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17404

AN:

152142

Hom.:

2029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0580

Gnomad EAS

AF:

0.0880

Gnomad SAS

AF:

0.0397

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0348

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.0460

AC:

26397

AN:

573336

Hom.:

1220

AF XY:

0.0436

AC XY:

13219

AN XY:

303480

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.0489

Gnomad4 ASJ exome

AF:

0.0607

Gnomad4 EAS exome

AF:

0.0691

Gnomad4 SAS exome

AF:

0.0341

Gnomad4 FIN exome

AF:

0.0286

Gnomad4 NFE exome

AF:

0.0334

Gnomad4 OTH exome

AF:

0.0619

GnomAD4 genome

AF:

0.115

AC:

17435

AN:

152260

Hom.:

2037

Cov.:

AF XY:

0.113

AC XY:

8441

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.0686

Gnomad4 ASJ

AF:

0.0580

Gnomad4 EAS

AF:

0.0882

Gnomad4 SAS

AF:

0.0395

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0348

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.0826

Hom.:

137

Bravo

AF:

0.127

Asia WGS

AF:

0.0820

AC:

286

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.6

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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