rs2106562

Variant names:

• chr7-20615645-C-G
• rs2106562
• NM_001163941.2:c.-214C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-20615645-C-G
• chr7-20615645-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 3 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163941.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	NM_001163941.2	MANE Select	c.-214C>G		upstream_gene	N/A	NP_001157413.1	Q2M3G0-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.-214C>G		upstream_gene	N/A	ENSP00000384881.2	Q2M3G0-4

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115103 AN: 150838 Hom.: 44299 Cov.: 27

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.: 66 Cov.: 0 AF XY: 0.713 AC XY: 127 AN XY: 178

African (AFR) AF: 0.900 AC: 9 AN: 10

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 6 AN: 6

East Asian (EAS) AF: 0.875 AC: 14 AN: 16

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.725 AC: 129 AN: 178

Other (OTH) AF: 0.700 AC: 7 AN: 10

GnomAD4 genome AF: 0.763 AC: 115212 AN: 150956 Hom.: 44347 Cov.: 27 AF XY: 0.762 AC XY: 56095 AN XY: 73640

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.44
PhyloP100		-0.67
PromoterAI		-0.0034	Neutral
Mutation Taster		=299/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2106562; hg19: chr7-20655268;