Variant rs1109867 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 ENST00000265316.9(ABCB6):c.-58C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 1,472,224 control chromosomes in the GnomAD database, including 565,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 48464 hom., cov: 36)

Exomes 𝑓: 0.88 ( 517178 hom. )

Consequence

ABCB6
ENST00000265316.9 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.124

Variant links:

Genes affected

ABCB6 (HGNC:47): (ATP binding cassette subfamily B member 6 (LAN blood group)) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ABC proteins transport various molecules across extra- and intra-cellular membranes. This protein is a member of the heavy metal importer subfamily and plays a role in porphyrin transport. This gene is the molecular basis of the Langereis (Lan) blood group antigen and mutations in this gene underlie familial pseudohyperkalemia and dyschromatosis universalis hereditaria. [provided by RefSeq, Mar 2017]

ABCB6 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=-0.79).

BP6

Variant 2-219218731-G-T is Benign according to our data. Variant chr2-219218731-G-T is described in ClinVar as [Benign]. Clinvar id is 1231199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCB6	NM_005689.4 linkuse as main transcript	c.-58C>A		5_prime_UTR_variant	1/19	ENST00000265316.9	NP_005680.1
ABCB6	NM_001349828.2 linkuse as main transcript	c.-58C>A		5_prime_UTR_variant	1/18		NP_001336757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCB6	ENST00000265316.9 linkuse as main transcript	c.-58C>A		5_prime_UTR_variant	1/19	1	NM_005689.4	ENSP00000265316	P1	Q9NP58-1
ABCB6	ENST00000295750.5 linkuse as main transcript	c.-58C>A		5_prime_UTR_variant	1/18	5		ENSP00000295750		Q9NP58-4

Frequencies

GnomAD3 genomes

AF:

0.776

AC:

118037

AN:

152128

Hom.:

48451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.898

Gnomad AMR

AF:

0.842

Gnomad ASJ

AF:

0.846

Gnomad EAS

AF:

0.843

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.953

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.902

Gnomad OTH

AF:

0.781

GnomAD4 exome

AF:

0.882

AC:

1164156

AN:

1319978

Hom.:

517178

Cov.:

AF XY:

0.881

AC XY:

567286

AN XY:

644082

show subpopulations

Gnomad4 AFR exome

AF:

0.452

Gnomad4 AMR exome

AF:

0.859

Gnomad4 ASJ exome

AF:

0.836

Gnomad4 EAS exome

AF:

0.842

Gnomad4 SAS exome

AF:

0.799

Gnomad4 FIN exome

AF:

0.951

Gnomad4 NFE exome

AF:

0.901

Gnomad4 OTH exome

AF:

0.847

GnomAD4 genome

AF:

0.776

AC:

118071

AN:

152246

Hom.:

48464

Cov.:

AF XY:

0.780

AC XY:

58071

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.478

Gnomad4 AMR

AF:

0.842

Gnomad4 ASJ

AF:

0.846

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.796

Gnomad4 FIN

AF:

0.953

Gnomad4 NFE

AF:

0.902

Gnomad4 OTH

AF:

0.782

Alfa

AF:

0.838

Hom.:

13013

Bravo

AF:

0.754

Asia WGS

AF:

0.818

AC:

2842

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	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.9

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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