Variant chr19-8302274-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_016579.4(CD320):c.*189G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 756,224 control chromosomes in the GnomAD database, including 3,302 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 2028 hom., cov: 33)

Exomes 𝑓: 0.046 ( 1274 hom. )

Consequence

CD320
NM_016579.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0440

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 19-8302274-C-T is Benign according to our data. Variant chr19-8302274-C-T is described in ClinVar as [Benign]. Clinvar id is 1239139.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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.*189G>A		3_prime_UTR_variant	5/5	ENST00000301458.10	NP_057663.1
CD320	NM_001165895.2 linkuse as main transcript	c.*189G>A		3_prime_UTR_variant	4/4		NP_001159367.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD320	ENST00000301458.10 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	5/5	1	NM_016579.4	ENSP00000301458	P1	Q9NPF0-1
CD320	ENST00000596002.5 linkuse as main transcript	c.*1326G>A	3_prime_UTR_variant, NMD_transcript_variant	5/5	1		ENSP00000471773
CD320	ENST00000537716.6 linkuse as main transcript	c.*189G>A	3_prime_UTR_variant	4/4	2		ENSP00000437697		Q9NPF0-2
CD320	ENST00000599573.1 linkuse as main transcript		downstream_gene_variant		2		ENSP00000471551

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17370

AN:

152098

Hom.:

2020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.0880

Gnomad SAS

AF:

0.0397

Gnomad FIN

AF:

0.0297

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0348

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0549

AC:

8506

AN:

154816

Hom.:

487

AF XY:

0.0513

AC XY:

4350

AN XY:

84850

show subpopulations

Gnomad AFR exome

AF:

0.306

Gnomad AMR exome

AF:

0.0456

Gnomad ASJ exome

AF:

0.0634

Gnomad EAS exome

AF:

0.0855

Gnomad SAS exome

AF:

0.0343

Gnomad FIN exome

AF:

0.0274

Gnomad NFE exome

AF:

0.0353

Gnomad OTH exome

AF:

0.0464

GnomAD4 exome

AF:

0.0458

AC:

27681

AN:

604008

Hom.:

1274

Cov.:

AF XY:

0.0433

AC XY:

14097

AN XY:

325296

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.0481

Gnomad4 ASJ exome

AF:

0.0610

Gnomad4 EAS exome

AF:

0.0679

Gnomad4 SAS exome

AF:

0.0342

Gnomad4 FIN exome

AF:

0.0281

Gnomad4 NFE exome

AF:

0.0334

Gnomad4 OTH exome

AF:

0.0612

GnomAD4 genome

AF:

0.114

AC:

17401

AN:

152216

Hom.:

2028

Cov.:

AF XY:

0.113

AC XY:

8430

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.0686

Gnomad4 ASJ

AF:

0.0579

Gnomad4 EAS

AF:

0.0882

Gnomad4 SAS

AF:

0.0395

Gnomad4 FIN

AF:

0.0297

Gnomad4 NFE

AF:

0.0348

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0521

Hom.:

311

Bravo

AF:

0.127

Asia WGS

AF:

0.0810

AC:

283

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.83

CADD

Benign

3.7

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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