Variant chr22-38989505-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004900.5(APOBEC3B):c.618T>C(p.Pro206Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00577 in 1,588,660 control chromosomes in the GnomAD database, including 776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 196 hom., cov: 30)

Exomes 𝑓: 0.0045 ( 580 hom. )

Consequence

APOBEC3B
NM_004900.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.97

Variant links:

Genes affected

APOBEC3B (HGNC:17352): (apolipoprotein B mRNA editing enzyme catalytic subunit 3B) This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. A hybrid gene results from the deletion of approximately 29.5 kb of sequence between this gene, APOBEC3B, and the adjacent gene APOBEC3A. The breakpoints of the deletion are within the two genes, so the deletion allele is predicted to have the promoter and coding region of APOBEC3A, but the 3' UTR of APOBEC3B. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

APOBEC3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 22-38989505-T-C is Benign according to our data. Variant chr22-38989505-T-C is described in ClinVar as [Benign]. Clinvar id is 777709.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.97 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3B	NM_004900.5 link	c.618T>C	p.Pro206Pro	synonymous_variant	5/8	ENST00000333467.4	NP_004891.5	Q9UH17-1
APOBEC3B	NM_001270411.2 link	c.618T>C	p.Pro206Pro	synonymous_variant	5/8		NP_001257340.2	Q9UH17-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
APOBEC3B	ENST00000333467.4 link	c.618T>C	p.Pro206Pro	synonymous_variant	5/8	1	NM_004900.5	ENSP00000327459.3	Q9UH17-1
APOBEC3B	ENST00000407298.7 link	c.618T>C	p.Pro206Pro	synonymous_variant	5/8	1		ENSP00000385068.3	Q9UH17-3
APOBEC3B	ENST00000335760.9 link	n.570-1827T>C		intron_variant		1		ENSP00000338897.5	Q9UH17-2
APOBEC3B	ENST00000402182.7 link	c.618T>C	p.Pro206Pro	synonymous_variant	5/7	2		ENSP00000385060.3	B0QYD3

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2715

AN:

148384

Hom.:

195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0555

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00837

Gnomad ASJ

AF:

0.00174

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0127

Gnomad FIN

AF:

0.00135

Gnomad MID

AF:

0.0131

Gnomad NFE

AF:

0.00326

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00756

AC:

1852

AN:

244828

Hom.:

180

AF XY:

0.00723

AC XY:

960

AN XY:

132710

show subpopulations

Gnomad AFR exome

AF:

0.0552

Gnomad AMR exome

AF:

0.00482

Gnomad ASJ exome

AF:

0.00339

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00989

Gnomad FIN exome

AF:

0.00280

Gnomad NFE exome

AF:

0.00335

Gnomad OTH exome

AF:

0.00564

GnomAD4 exome

AF:

0.00448

AC:

6455

AN:

1440206

Hom.:

580

Cov.:

AF XY:

0.00480

AC XY:

3434

AN XY:

715954

show subpopulations

Gnomad4 AFR exome

AF:

0.0581

Gnomad4 AMR exome

AF:

0.00505

Gnomad4 ASJ exome

AF:

0.00315

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.0111

Gnomad4 FIN exome

AF:

0.00186

Gnomad4 NFE exome

AF:

0.00244

Gnomad4 OTH exome

AF:

0.00741

GnomAD4 genome

AF:

0.0183

AC:

2719

AN:

148454

Hom.:

196

Cov.:

AF XY:

0.0183

AC XY:

1325

AN XY:

72248

show subpopulations

Gnomad4 AFR

AF:

0.0554

Gnomad4 AMR

AF:

0.00837

Gnomad4 ASJ

AF:

0.00174

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0128

Gnomad4 FIN

AF:

0.00135

Gnomad4 NFE

AF:

0.00326

Gnomad4 OTH

AF:

0.0163

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.0205

Asia WGS

AF:

0.00612

AC:

AN:

3116

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	Labcorp Genetics (formerly Invitae), Labcorp	Nov 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.1

DANN

Benign

0.54

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