chr2-219210071-T-A

Position:

• chr2-219210071-T-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_005689.4(ABCB6):​c.2421-25A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,609,958 control chromosomes in the GnomAD database, including 773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.038 (206 hom., cov: 32)
  • Exomes 𝑓: 0.017 (567 hom.)
• Consequence: ABCB6 NM_005689.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.51

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 2-219210071-T-A is Benign according to our data. Variant chr2-219210071-T-A is described in ClinVar as [Benign]. Clinvar id is 1242799.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB6	NM_005689.4	c.2421-25A>T		intron_variant		ENST00000265316.9
ABCB6	NM_001349828.2	c.2283-25A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB6	ENST00000265316.9	c.2421-25A>T		intron_variant		1	NM_005689.4	P1

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5721 AN: 151930 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0282

GnomAD3 exomes AF: 0.0267 AC: 6703 AN: 251252 Hom.: 240 AF XY: 0.0249 AC XY: 3386 AN XY: 135808

Gnomad AFR exome AF: 0.0874

Gnomad AMR exome AF: 0.00775

Gnomad ASJ exome AF: 0.0214

Gnomad EAS exome AF: 0.108

Gnomad SAS exome AF: 0.0130

Gnomad FIN exome AF: 0.0334

Gnomad NFE exome AF: 0.0138

Gnomad OTH exome AF: 0.0214

GnomAD4 exome AF: 0.0169 AC: 24648 AN: 1457910 Hom.: 567 Cov.: 29 AF XY: 0.0165 AC XY: 11979 AN XY: 725602

Gnomad4 AFR exome AF: 0.0868

Gnomad4 AMR exome AF: 0.00859

Gnomad4 ASJ exome AF: 0.0198

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.0124

Gnomad4 FIN exome AF: 0.0308

Gnomad4 NFE exome AF: 0.0111

Gnomad4 OTH exome AF: 0.0225

GnomAD4 genome AF: 0.0377 AC: 5736 AN: 152048 Hom.: 206 Cov.: 32 AF XY: 0.0387 AC XY: 2878 AN XY: 74316

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0135

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0142

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0132 Hom.: 10

Bravo AF: 0.0383

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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

Other links and lift over

dbSNP: rs73993544; hg19: chr2-220074793;