dbSNP rs879459: ABCC3:c.1871-79C>T (chr17-50668774-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003786.4(ABCC3):c.1871-79C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 1,212,150 control chromosomes in the GnomAD database, including 446,664 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 0.83 ( 52035 hom., cov: 27)

Exomes 𝑓: 0.86 ( 394629 hom. )

Consequence

ABCC3
NM_003786.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.805

Publications

2 publications found

Variant links:

Genes affected

ABCC3 (HGNC:54): (ATP binding cassette subfamily C member 3) The 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 MRP subfamily which is involved in multi-drug resistance. The specific function of this protein has not yet been determined; however, this protein may play a role in the transport of biliary and intestinal excretion of organic anions. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ABCC3 links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC3	NM_003786.4 link	c.1871-79C>T		intron_variant	Intron 14 of 30	ENST00000285238.13	NP_003777.2	O15438-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ABCC3	ENST00000285238.13 link	c.1871-79C>T	intron_variant	Intron 14 of 30	1	NM_003786.4	ENSP00000285238.8	O15438-1
ABCC3	ENST00000502426.5 link	n.*393-79C>T	intron_variant	Intron 14 of 29	2		ENSP00000427073.1	O15438-3
ABCC3	ENST00000503304.1 link	n.88+257C>T	intron_variant	Intron 1 of 3	5
ABCC3	ENST00000505699.5 link	n.1871-79C>T	intron_variant	Intron 14 of 29	2		ENSP00000427521.1	O15438-2

Frequencies

GnomAD3 genomes

AF:

0.827

AC:

125226

AN:

151366

Hom.:

52006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.825

Gnomad AMR

AF:

0.843

Gnomad ASJ

AF:

0.852

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.895

Gnomad FIN

AF:

0.821

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.855

Gnomad OTH

AF:

0.836

GnomAD4 exome

AF:

0.861

AC:

913333

AN:

1060666

Hom.:

394629

AF XY:

0.863

AC XY:

466860

AN XY:

541188

show subpopulations

African (AFR)

AF:

0.795

AC:

20185

AN:

25386

American (AMR)

AF:

0.879

AC:

34145

AN:

38826

Ashkenazi Jewish (ASJ)

AF:

0.852

AC:

19622

AN:

23032

East Asian (EAS)

AF:

0.726

AC:

26474

AN:

36442

South Asian (SAS)

AF:

0.909

AC:

68555

AN:

75392

European-Finnish (FIN)

AF:

0.812

AC:

41456

AN:

51026

Middle Eastern (MID)

AF:

0.904

AC:

4535

AN:

5014

European-Non Finnish (NFE)

AF:

0.868

AC:

658624

AN:

758514

Other (OTH)

AF:

0.845

AC:

39737

AN:

47034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

6597

13195

19792

26390

32987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.827

AC:

125309

AN:

151484

Hom.:

52035

Cov.:

AF XY:

0.827

AC XY:

61183

AN XY:

73998

show subpopulations

African (AFR)

AF:

0.787

AC:

32415

AN:

41190

American (AMR)

AF:

0.843

AC:

12835

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.852

AC:

2955

AN:

3470

East Asian (EAS)

AF:

0.667

AC:

3400

AN:

5098

South Asian (SAS)

AF:

0.895

AC:

4284

AN:

4788

European-Finnish (FIN)

AF:

0.821

AC:

8626

AN:

10510

Middle Eastern (MID)

AF:

0.901

AC:

265

AN:

294

European-Non Finnish (NFE)

AF:

0.855

AC:

58018

AN:

67896

Other (OTH)

AF:

0.837

AC:

1760

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

1074

2147

3221

4294

5368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.837

Hom.:

6654

Bravo

AF:

0.826

Asia WGS

AF:

0.813

AC:

2830

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.79

(source)

DANN

Benign

0.50

PhyloP100

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs879459

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