rs7296418

chr12-122973072-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000542678.5(ABCB9):c.-88+5826G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,132 control chromosomes in the GnomAD database, including 36,508 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.69 (36499 hom., cov: 32)
  • Exomes 𝑓: 0.73 (9 hom.)
• Consequence: ABCB9 ENST00000542678.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

ABCB9 (HGNC:50): (ATP binding cassette subfamily B member 9) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance as well as antigen presentation. This family member functions in the translocation of peptides from the cytosol into the lysosomal lumen. Alternative splicing of this gene results in distinct isoforms which are likely to have different substrate specificities. [provided by RefSeq, Jul 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB9	XM_017019103.2	c.-117G>A		5_prime_UTR_variant	2/13
ABCB9	XM_011538095.3	c.-88+1643G>A		intron_variant
ABCB9	XM_011538096.3	c.-88+1443G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB9	ENST00000542678.5	c.-88+5826G>A		intron_variant		1		P1
ABCB9	ENST00000543935.1	c.-117G>A		5_prime_UTR_variant	2/3	4
ABCB9	ENST00000392439.7	c.-88+1643G>A		intron_variant		5		P1
ABCB9	ENST00000622723.1	n.162G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105071 AN: 151984 Hom.: 36478 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.689

GnomAD4 exome AF: 0.733 AC: 22 AN: 30 Hom.: 9 Cov.: 0 AF XY: 0.667 AC XY: 16 AN XY: 24

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 0.688

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.691 AC: 105136 AN: 152102 Hom.: 36499 Cov.: 32 AF XY: 0.690 AC XY: 51308 AN XY: 74358

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.687

Alfa AF: 0.700 Hom.: 49552

Bravo AF: 0.686

Asia WGS AF: 0.608 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.51
Dann	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7296418; hg19: chr12-123457619;