Genetic Variant NM_000443.4:c.504C>T (chr7-87452976-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000443.4(ABCB4):c.504C>T(p.Asn168Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 1,613,056 control chromosomes in the GnomAD database, including 228,424 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 16457 hom., cov: 31)

Exomes 𝑓: 0.53 ( 211967 hom. )

Consequence

ABCB4
NM_000443.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -0.744

Publications

71 publications found

Variant links:

Genes affected

ABCB4 (HGNC:45): (ATP binding cassette subfamily B member 4) 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 gene encodes a full transporter and member of the p-glycoprotein family of membrane proteins with phosphatidylcholine as its substrate. The function of this protein has not yet been determined; however, it may involve transport of phospholipids from liver hepatocytes into bile. Alternative splicing of this gene results in several products of undetermined function. [provided by RefSeq, Jul 2008]

ABCB4 Gene-Disease associations (from GenCC):

progressive familial intrahepatic cholestasis type 3
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
gallbladder disease 1
Inheritance: SD, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
pancreatitis
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ABCB4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 7-87452976-G-A is Benign according to our data. Variant chr7-87452976-G-A is described in ClinVar as Benign. ClinVar VariationId is 198082.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.744 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000443.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ABCB4	NM_000443.4	MANE Select	c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 28	NP_000434.1	P21439-2
ABCB4	NM_018849.3		c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 28	NP_061337.1	P21439-1
ABCB4	NM_018850.3		c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 27	NP_061338.1	P21439-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ABCB4	ENST00000649586.2	MANE Select	c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 28	ENSP00000496956.2	P21439-2
ABCB4	ENST00000265723.8	TSL:1	c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 28	ENSP00000265723.4	P21439-1
ABCB4	ENST00000359206.8	TSL:1	c.504C>T	p.Asn168Asn	synonymous	Exon 6 of 28	ENSP00000352135.3	P21439-2

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63467

AN:

151800

Hom.:

16462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.651

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.430

GnomAD2 exomes

AF:

0.480

AC:

120567

AN:

251264

AF XY:

0.489

show subpopulations

Gnomad AFR exome

AF:

0.0937

Gnomad AMR exome

AF:

0.422

Gnomad ASJ exome

AF:

0.393

Gnomad EAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.639

Gnomad NFE exome

AF:

0.558

Gnomad OTH exome

AF:

0.490

GnomAD4 exome

AF:

0.530

AC:

775002

AN:

1461138

Hom.:

211967

Cov.:

AF XY:

0.529

AC XY:

384772

AN XY:

726898

show subpopulations

African (AFR)

AF:

0.0833

AC:

2790

AN:

33476

American (AMR)

AF:

0.434

AC:

19396

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

10112

AN:

26122

East Asian (EAS)

AF:

0.393

AC:

15601

AN:

39690

South Asian (SAS)

AF:

0.442

AC:

38128

AN:

86240

European-Finnish (FIN)

AF:

0.637

AC:

34025

AN:

53394

Middle Eastern (MID)

AF:

0.437

AC:

2523

AN:

5768

European-Non Finnish (NFE)

AF:

0.561

AC:

623410

AN:

1111366

Other (OTH)

AF:

0.481

AC:

29017

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

19386

38772

58157

77543

96929

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17124

34248

51372

68496

85620

<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:

0.418

AC:

63447

AN:

151918

Hom.:

16457

Cov.:

AF XY:

0.422

AC XY:

31368

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.105

AC:

4341

AN:

41410

American (AMR)

AF:

0.489

AC:

7466

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1380

AN:

3468

East Asian (EAS)

AF:

0.382

AC:

1968

AN:

5154

South Asian (SAS)

AF:

0.443

AC:

2126

AN:

4804

European-Finnish (FIN)

AF:

0.651

AC:

6873

AN:

10556

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.554

AC:

37665

AN:

67958

Other (OTH)

AF:

0.429

AC:

905

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1569

3138

4708

6277

7846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.503

Hom.:

84674

Bravo

AF:

0.388

Asia WGS

AF:

0.410

AC:

1427

AN:

3478

EpiCase

AF:

0.541

EpiControl

AF:

0.545

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (5)

Cholestasis, intrahepatic, of pregnancy, 3 (2)

not provided (2)

Progressive familial intrahepatic cholestasis type 3 (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.67

(source)

DANN

Benign

0.60

PhyloP100

-0.74

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

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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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over