rs2270788

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019625.4(ABCB9):​c.*109A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,429,832 control chromosomes in the GnomAD database, including 21,843 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 0.25 ( 8392 hom., cov: 31)
Exomes 𝑓: 0.12 ( 13451 hom. )

Consequence

ABCB9
NM_019625.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCB9NM_019625.4 linkuse as main transcriptc.*109A>G 3_prime_UTR_variant 12/12 ENST00000280560.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCB9ENST00000280560.13 linkuse as main transcriptc.*109A>G 3_prime_UTR_variant 12/121 NM_019625.4 P1Q9NP78-1

Frequencies

GnomAD3 genomes
AF:
0.247
AC:
37556
AN:
151890
Hom.:
8348
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.600
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.160
Gnomad ASJ
AF:
0.0700
Gnomad EAS
AF:
0.204
Gnomad SAS
AF:
0.163
Gnomad FIN
AF:
0.101
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0976
Gnomad OTH
AF:
0.208
GnomAD4 exome
AF:
0.118
AC:
150849
AN:
1277824
Hom.:
13451
Cov.:
34
AF XY:
0.118
AC XY:
72743
AN XY:
617896
show subpopulations
Gnomad4 AFR exome
AF:
0.622
Gnomad4 AMR exome
AF:
0.138
Gnomad4 ASJ exome
AF:
0.0706
Gnomad4 EAS exome
AF:
0.208
Gnomad4 SAS exome
AF:
0.156
Gnomad4 FIN exome
AF:
0.0951
Gnomad4 NFE exome
AF:
0.0984
Gnomad4 OTH exome
AF:
0.144
GnomAD4 genome
AF:
0.248
AC:
37666
AN:
152008
Hom.:
8392
Cov.:
31
AF XY:
0.245
AC XY:
18179
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.601
Gnomad4 AMR
AF:
0.160
Gnomad4 ASJ
AF:
0.0700
Gnomad4 EAS
AF:
0.204
Gnomad4 SAS
AF:
0.162
Gnomad4 FIN
AF:
0.101
Gnomad4 NFE
AF:
0.0976
Gnomad4 OTH
AF:
0.214
Alfa
AF:
0.120
Hom.:
3385
Bravo
AF:
0.271
Asia WGS
AF:
0.252
AC:
876
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.7
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs2270788; hg19: chr12-123414349; COSMIC: COSV54893683; COSMIC: COSV54893683; API