dbSNP rs2303922: ABCB8:c.95+25A>C (chr7-151028635-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_007188.5(ABCB8):c.95+25A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 1,604,200 control chromosomes in the GnomAD database, including 110,374 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 0.39 ( 12196 hom., cov: 33)

Exomes 𝑓: 0.36 ( 98178 hom. )

Consequence

ABCB8
NM_007188.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.644

Publications

17 publications found

Variant links:

Genes affected

ABCB8 (HGNC:49): (ATP binding cassette subfamily B member 8) This nuclear gene encodes a multi-pass membrane protein that is targeted to the mitochondrial inner membrane. The encoded protein is an ATP-dependent transporter that may mediate the passage of organic and inorganic molecules out of the mitochondria. Loss of function of the related gene in mouse results in a disruption of iron homeostasis between the mitochondria and cytosol. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ABCB8 links:

ENSG00000243433 (HGNC:):

ENSG00000243433 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007188.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCB8	NM_007188.5	MANE Select	c.95+25A>C	intron	N/A	NP_009119.2	Q9NUT2-2
ABCB8	NM_001282291.2		c.95+25A>C	intron	N/A	NP_001269220.1	Q9NUT2-1
ABCB8	NM_001282292.2		c.95+25A>C	intron	N/A	NP_001269221.1	Q9NUT2-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCB8	ENST00000358849.9	TSL:1 MANE Select	c.95+25A>C	intron	N/A	ENSP00000351717.4	Q9NUT2-2
ABCB8	ENST00000498578.5	TSL:1	c.95+25A>C	intron	N/A	ENSP00000418271.1	Q9NUT2-3
ABCB8	ENST00000879589.1		c.95+25A>C	intron	N/A	ENSP00000549648.1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59720

AN:

151952

Hom.:

12176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.379

GnomAD2 exomes

AF:

0.342

AC:

79296

AN:

231842

AF XY:

0.345

show subpopulations

Gnomad AFR exome

AF:

0.525

Gnomad AMR exome

AF:

0.209

Gnomad ASJ exome

AF:

0.362

Gnomad EAS exome

AF:

0.290

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.354

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.364

AC:

529135

AN:

1452130

Hom.:

98178

Cov.:

AF XY:

0.365

AC XY:

263287

AN XY:

721814

show subpopulations

African (AFR)

AF:

0.525

AC:

17523

AN:

33354

American (AMR)

AF:

0.213

AC:

9277

AN:

43482

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

9356

AN:

26030

East Asian (EAS)

AF:

0.310

AC:

12228

AN:

39408

South Asian (SAS)

AF:

0.391

AC:

33299

AN:

85148

European-Finnish (FIN)

AF:

0.336

AC:

17177

AN:

51162

Middle Eastern (MID)

AF:

0.325

AC:

1516

AN:

4660

European-Non Finnish (NFE)

AF:

0.367

AC:

406723

AN:

1108936

Other (OTH)

AF:

0.368

AC:

22036

AN:

59950

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

19135

38271

57406

76542

95677

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13000

26000

39000

52000

65000

<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:

0.393

AC:

59788

AN:

152070

Hom.:

12196

Cov.:

AF XY:

0.386

AC XY:

28716

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.518

AC:

21493

AN:

41484

American (AMR)

AF:

0.284

AC:

4351

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1220

AN:

3470

East Asian (EAS)

AF:

0.288

AC:

1480

AN:

5134

South Asian (SAS)

AF:

0.388

AC:

1866

AN:

4814

European-Finnish (FIN)

AF:

0.333

AC:

3531

AN:

10594

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.362

AC:

24617

AN:

67962

Other (OTH)

AF:

0.380

AC:

804

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1855

3709

5564

7418

9273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.358

Hom.:

19124

Bravo

AF:

0.393

Asia WGS

AF:

0.363

AC:

1262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.3

(source)

DANN

Benign

0.65

PhyloP100

-0.64

PromoterAI

-0.041

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over