2-219217782-C-T

Position:

chr2-219217782-C-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM5BP4_StrongBP6_Very_StrongBS1BS2

The NM_005689.4(ABCB6):c.575G>A(p.Arg192Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00368 in 1,613,524 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R192W) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0038 ( 16 hom. )

Consequence

ABCB6
NM_005689.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:11

Conservation

PhyloP100: 5.42

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM5

Other missense variant is known to change same aminoacid residue: Variant chr2-219217783-G-A is described in Lovd as [Pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.027407736).

BP6

Variant 2-219217782-C-T is Benign according to our data. Variant chr2-219217782-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 68473.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-219217782-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.003 (456/152234) while in subpopulation NFE AF= 0.00454 (309/68002). AF 95% confidence interval is 0.00413. There are 0 homozygotes in gnomad4. There are 200 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 456 AD,BG gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCB6	NM_005689.4 linkuse as main transcript	c.575G>A	p.Arg192Gln	missense_variant	2/19	ENST00000265316.9	NP_005680.1
ABCB6	NM_001349828.2 linkuse as main transcript	c.549+343G>A		intron_variant			NP_001336757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCB6	ENST00000265316.9 linkuse as main transcript	c.575G>A	p.Arg192Gln	missense_variant	2/19	1	NM_005689.4	ENSP00000265316	P1	Q9NP58-1

Frequencies

GnomAD3 genomes

AF:

0.00300

AC:

456

AN:

152116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000773

Gnomad AMI

AF:

0.00769

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00635

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00454

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00345

AC:

864

AN:

250726

Hom.:

AF XY:

0.00345

AC XY:

468

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.00445

Gnomad ASJ exome

AF:

0.00825

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00108

Gnomad FIN exome

AF:

0.00194

Gnomad NFE exome

AF:

0.00445

Gnomad OTH exome

AF:

0.00639

GnomAD4 exome

AF:

0.00375

AC:

5485

AN:

1461290

Hom.:

Cov.:

AF XY:

0.00369

AC XY:

2681

AN XY:

726986

show subpopulations

Gnomad4 AFR exome

AF:

0.000479

Gnomad4 AMR exome

AF:

0.00420

Gnomad4 ASJ exome

AF:

0.00758

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000940

Gnomad4 FIN exome

AF:

0.00223

Gnomad4 NFE exome

AF:

0.00412

Gnomad4 OTH exome

AF:

0.00416

GnomAD4 genome

AF:

0.00300

AC:

456

AN:

152234

Hom.:

Cov.:

AF XY:

0.00269

AC XY:

200

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00320

Gnomad4 ASJ

AF:

0.00635

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00454

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00456

Hom.:

Bravo

AF:

0.00311

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00419

AC:

ExAC

AF:

0.00342

AC:

415

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00529

EpiControl

AF:

0.00539

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:6

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 22, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2023	ABCB6: BS2 -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Microphthalmia, isolated, with coloboma 7

Uncertain:1Benign:1

Benign, no assertion criteria provided	clinical testing	Dr.Nikuei Genetic Center	-	- -
Uncertain significance, no assertion criteria provided	research	Eye Genetics Research Group, Children's Medical Research Institute	Mar 30, 2012	- -

Acute intermittent porphyria

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Phillips Lab, Hematology, University of Utah

Aug 16, 2021

- -

Variegate porphyria

Benign:1

Benign, criteria provided, single submitter

clinical testing

Phillips Lab, Hematology, University of Utah

Aug 16, 2021

- -

ABCB6-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 25, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Protoporphyria, erythropoietic, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Phillips Lab, Hematology, University of Utah

Aug 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.066

BayesDel_noAF

Uncertain

0.13

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.85

Eigen

Pathogenic

0.74

Eigen_PC

Pathogenic

0.75

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.88

M_CAP

Uncertain

0.21

MetaRNN

Benign

0.027

MetaSVM

Uncertain

0.67

MutationAssessor

Benign

1.8

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-3.0

REVEL

Pathogenic

0.72

Sift

Uncertain

0.0060

Sift4G

Uncertain

0.017

Polyphen

0.98

Vest4

0.78

MVP

0.97

MPC

0.69

ClinPred

0.041

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.41

gMVP

0.85

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