Genetic Variant NM_001163941.2:c.-214C>G (chr7-20615645-C-G) – 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.-214C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 151,182 control chromosomes in the GnomAD database, including 44,413 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 0.76 ( 44347 hom., cov: 27)

Exomes 𝑓: 0.74 ( 66 hom. )

Consequence

ABCB5
NM_001163941.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.668

Publications

3 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:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2 link	c.-214C>G		upstream_gene_variant		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.-214C>G		upstream_gene_variant		1	NM_001163941.2	ENSP00000384881.2		Q2M3G0-4

Frequencies

GnomAD3 genomes

AF:

0.763

AC:

115103

AN:

150838

Hom.:

44299

Cov.:

show subpopulations

Gnomad AFR

AF:

0.850

Gnomad AMI

AF:

0.772

Gnomad AMR

AF:

0.809

Gnomad ASJ

AF:

0.709

Gnomad EAS

AF:

0.872

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.698

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.758

GnomAD4 exome

AF:

0.739

AC:

167

AN:

226

Hom.:

Cov.:

AF XY:

0.713

AC XY:

127

AN XY:

178

show subpopulations

African (AFR)

AF:

0.900

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.875

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.725

AC:

129

AN:

178

Other (OTH)

AF:

0.700

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.551

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.763

AC:

115212

AN:

150956

Hom.:

44347

Cov.:

AF XY:

0.762

AC XY:

56095

AN XY:

73640

show subpopulations

African (AFR)

AF:

0.849

AC:

34829

AN:

41000

American (AMR)

AF:

0.809

AC:

12281

AN:

15176

Ashkenazi Jewish (ASJ)

AF:

0.709

AC:

2457

AN:

3464

East Asian (EAS)

AF:

0.871

AC:

4470

AN:

5132

South Asian (SAS)

AF:

0.687

AC:

3267

AN:

4754

European-Finnish (FIN)

AF:

0.698

AC:

7204

AN:

10320

Middle Eastern (MID)

AF:

0.609

AC:

179

AN:

294

European-Non Finnish (NFE)

AF:

0.711

AC:

48247

AN:

67822

Other (OTH)

AF:

0.756

AC:

1574

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1302

2604

3907

5209

6511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

848

1696

2544

3392

4240

<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:

0.645

Hom.:

1816

Bravo

AF:

0.778

Asia WGS

AF:

0.759

AC:

2637

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.56

(source)

DANN

Benign

0.44

PhyloP100

-0.67

PromoterAI

-0.0034

Neutral

(source)

Mutation Taster

=299/1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over