Genetic Variant ABCC13:n.1041G>A (chr21-14299523-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 ENST00000467409.7(ABCC13):n.1041G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 456,608 control chromosomes in the GnomAD database, including 4,480 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 0.12 ( 1235 hom., cov: 32)

Exomes 𝑓: 0.14 ( 3245 hom. )

Consequence

ABCC13
ENST00000467409.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

11 publications found

Variant links:

Genes affected

ABCC13 (HGNC:):

ABCC13 links:

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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC13	NR_003087.1 link	n.976G>A		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ABCC13	ENST00000467409.7 link	n.1041G>A	non_coding_transcript_exon_variant	Exon 6 of 6	1
ABCC13	ENST00000481582.5 link	n.3918G>A	non_coding_transcript_exon_variant	Exon 5 of 5	1
ABCC13	ENST00000482980.5 link	n.891-6173G>A	intron_variant	Intron 5 of 13	1

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18143

AN:

152074

Hom.:

1235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0624

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.00923

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.122

GnomAD2 exomes

AF:

0.122

AC:

17074

AN:

139554

AF XY:

0.124

show subpopulations

Gnomad AFR exome

AF:

0.0578

Gnomad AMR exome

AF:

0.0750

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.00847

Gnomad FIN exome

AF:

0.166

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.134

GnomAD4 exome

AF:

0.136

AC:

41390

AN:

304416

Hom.:

3245

Cov.:

AF XY:

0.135

AC XY:

23410

AN XY:

173340

show subpopulations

African (AFR)

AF:

0.0585

AC:

505

AN:

8626

American (AMR)

AF:

0.0729

AC:

1990

AN:

27280

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

2079

AN:

10790

East Asian (EAS)

AF:

0.00923

AC:

AN:

9210

South Asian (SAS)

AF:

0.120

AC:

7151

AN:

59738

European-Finnish (FIN)

AF:

0.171

AC:

2194

AN:

12796

Middle Eastern (MID)

AF:

0.145

AC:

403

AN:

2784

European-Non Finnish (NFE)

AF:

0.157

AC:

25015

AN:

158948

Other (OTH)

AF:

0.138

AC:

1968

AN:

14244

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

2163

4325

6488

8650

10813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.119

AC:

18136

AN:

152192

Hom.:

1235

Cov.:

AF XY:

0.118

AC XY:

8761

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0623

AC:

2586

AN:

41522

American (AMR)

AF:

0.100

AC:

1529

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

647

AN:

3468

East Asian (EAS)

AF:

0.00926

AC:

AN:

5186

South Asian (SAS)

AF:

0.114

AC:

549

AN:

4826

European-Finnish (FIN)

AF:

0.173

AC:

1833

AN:

10574

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.155

AC:

10555

AN:

68014

Other (OTH)

AF:

0.121

AC:

256

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

816

1633

2449

3266

4082

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.144

Hom.:

4533

Bravo

AF:

0.110

Asia WGS

AF:

0.0520

AC:

181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.1

(source)

DANN

Benign

0.80

PhyloP100

1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over