dbSNP rs78414512: ABCB5:c.109-34C>A (chr7-20628654-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001163941.2(ABCB5):c.109-34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,590,304 control chromosomes in the GnomAD database, including 16,061 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 0.11 ( 1208 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14853 hom. )

Consequence

ABCB5
NM_001163941.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.07

Publications

6 publications found

Variant links:

Genes affected

ABCB5 (HGNC:46): (ATP binding cassette subfamily B member 5) ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM, Mar 2008]

ABCB5 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2 link	c.109-34C>A		intron_variant	Intron 3 of 27	ENST00000404938.7	NP_001157413.1	Q2M3G0-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7 link	c.109-34C>A		intron_variant	Intron 3 of 27	1	NM_001163941.2	ENSP00000384881.2		Q2M3G0-4

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16516

AN:

151010

Hom.:

1208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0259

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.0981

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.000788

Gnomad SAS

AF:

0.0608

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.0976

GnomAD2 exomes

AF:

0.113

AC:

25715

AN:

226808

AF XY:

0.116

show subpopulations

Gnomad AFR exome

AF:

0.0214

Gnomad AMR exome

AF:

0.0624

Gnomad ASJ exome

AF:

0.124

Gnomad EAS exome

AF:

0.00191

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.124

GnomAD4 exome

AF:

0.137

AC:

197309

AN:

1439172

Hom.:

14853

Cov.:

AF XY:

0.136

AC XY:

96967

AN XY:

713988

show subpopulations

African (AFR)

AF:

0.0187

AC:

621

AN:

33148

American (AMR)

AF:

0.0661

AC:

2773

AN:

41950

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

3245

AN:

25620

East Asian (EAS)

AF:

0.00108

AC:

AN:

39066

South Asian (SAS)

AF:

0.0704

AC:

5881

AN:

83500

European-Finnish (FIN)

AF:

0.222

AC:

11578

AN:

52184

Middle Eastern (MID)

AF:

0.107

AC:

600

AN:

5622

European-Non Finnish (NFE)

AF:

0.150

AC:

165085

AN:

1098618

Other (OTH)

AF:

0.126

AC:

7484

AN:

59464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

8271

16542

24812

33083

41354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5700

11400

17100

22800

28500

<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:

0.109

AC:

16515

AN:

151132

Hom.:

1208

Cov.:

AF XY:

0.111

AC XY:

8199

AN XY:

73832

show subpopulations

African (AFR)

AF:

0.0259

AC:

1066

AN:

41236

American (AMR)

AF:

0.0979

AC:

1482

AN:

15142

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

433

AN:

3452

East Asian (EAS)

AF:

0.000790

AC:

AN:

5062

South Asian (SAS)

AF:

0.0612

AC:

292

AN:

4768

European-Finnish (FIN)

AF:

0.225

AC:

2363

AN:

10480

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.155

AC:

10477

AN:

67704

Other (OTH)

AF:

0.0966

AC:

202

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

713

1427

2140

2854

3567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.133

Hom.:

300

Bravo

AF:

0.0950

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.050

(source)

DANN

Benign

0.52

PhyloP100

-3.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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