dbSNP rs2822618: ABCC13:n.2848-7G>A (chr21-14353547-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000463099.1(ABCC13):n.2848-7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,444 control chromosomes in the GnomAD database, including 24,963 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 0.57 ( 24905 hom., cov: 32)

Exomes 𝑓: 0.52 ( 58 hom. )

Consequence

ABCC13
ENST00000463099.1 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.139

Publications

3 publications found

Variant links:

Genes affected

ABCC13 (HGNC:16022): (ATP binding cassette subfamily C member 13 (pseudogene)) This gene is a member of the superfamily of genes encoding 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, and White). This family member is part of the MRP subfamily, which is involved in multi-drug resistance, but the human locus is now thought to be a pseudogene incapable of encoding a functional ABC protein. Alternative splicing results in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

ABCC13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463099.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC13	ENST00000463099.1	TSL:6	n.2848-7G>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

86008

AN:

151890

Hom.:

24870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.691

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.595

Gnomad SAS

AF:

0.527

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.582

GnomAD4 exome

AF:

0.518

AC:

226

AN:

436

Hom.:

Cov.:

AF XY:

0.477

AC XY:

126

AN XY:

264

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.514

AC:

219

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.566

AC:

86088

AN:

152008

Hom.:

24905

Cov.:

AF XY:

0.563

AC XY:

41795

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.691

AC:

28667

AN:

41466

American (AMR)

AF:

0.516

AC:

7881

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.589

AC:

2042

AN:

3468

East Asian (EAS)

AF:

0.594

AC:

3075

AN:

5174

South Asian (SAS)

AF:

0.527

AC:

2541

AN:

4826

European-Finnish (FIN)

AF:

0.473

AC:

4997

AN:

10562

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.515

AC:

34982

AN:

67930

Other (OTH)

AF:

0.585

AC:

1234

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1906

3811

5717

7622

9528

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

728

1456

2184

2912

3640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.533

Hom.:

94119

Bravo

AF:

0.576

Asia WGS

AF:

0.608

AC:

2115

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.42

(source)

DANN

Benign

0.24

PhyloP100

0.14

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over