Variant chr7-151034432-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_007188.5(ABCB8):c.564+4C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,613,872 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 42 hom., cov: 33)

Exomes 𝑓: 0.0029 ( 65 hom. )

Consequence

ABCB8
NM_007188.5 splice_donor_region, intron

Scores

Splicing: ADA: 0.0002467

Clinical Significance

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

Conservation

PhyloP100: -0.144

Variant links:

Genes affected

ABCB8 (HGNC:49): (ATP binding cassette subfamily B member 8) This nuclear gene encodes a multi-pass membrane protein that is targeted to the mitochondrial inner membrane. The encoded protein is an ATP-dependent transporter that may mediate the passage of organic and inorganic molecules out of the mitochondria. Loss of function of the related gene in mouse results in a disruption of iron homeostasis between the mitochondria and cytosol. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ABCB8 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=-0.69).

BP6

Variant 7-151034432-C-T is Benign according to our data. Variant chr7-151034432-C-T is described in ClinVar as [Benign]. Clinvar id is 773219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
ABCB8	NM_007188.5 linkuse as main transcript	c.564+4C>T	splice_donor_region_variant, intron_variant	ENST00000358849.9
ABCB8	NM_001282291.2 linkuse as main transcript	c.615+4C>T	splice_donor_region_variant, intron_variant
ABCB8	NM_001282292.2 linkuse as main transcript	c.564+4C>T	splice_donor_region_variant, intron_variant
ABCB8	NM_001282293.2 linkuse as main transcript	c.300+4C>T	splice_donor_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB8	ENST00000358849.9 linkuse as main transcript	c.564+4C>T		splice_donor_region_variant, intron_variant		1	NM_007188.5	P1	Q9NUT2-2

Frequencies

GnomAD3 genomes

AF:

0.0160

AC:

2434

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0535

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00517

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00327

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00107

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00545

AC:

1368

AN:

250954

Hom.:

AF XY:

0.00463

AC XY:

628

AN XY:

135650

show subpopulations

Gnomad AFR exome

AF:

0.0541

Gnomad AMR exome

AF:

0.00312

Gnomad ASJ exome

AF:

0.000797

Gnomad EAS exome

AF:

0.00348

Gnomad SAS exome

AF:

0.00614

Gnomad FIN exome

AF:

0.000187

Gnomad NFE exome

AF:

0.000863

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00293

AC:

4278

AN:

1461592

Hom.:

Cov.:

AF XY:

0.00285

AC XY:

2075

AN XY:

727092

show subpopulations

Gnomad4 AFR exome

AF:

0.0569

Gnomad4 AMR exome

AF:

0.00340

Gnomad4 ASJ exome

AF:

0.000460

Gnomad4 EAS exome

AF:

0.00146

Gnomad4 SAS exome

AF:

0.00585

Gnomad4 FIN exome

AF:

0.000169

Gnomad4 NFE exome

AF:

0.00118

Gnomad4 OTH exome

AF:

0.00515

GnomAD4 genome

AF:

0.0160

AC:

2433

AN:

152280

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1188

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0533

Gnomad4 AMR

AF:

0.00516

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00328

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00107

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00525

Hom.:

Bravo

AF:

0.0177

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.00125

EpiControl

AF:

0.000948

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 08, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

8.6

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00025

dbscSNV1_RF

Benign

0.040

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