rs17143258

Variant names:

• chr7-20686998-C-T
• rs17143258
• NM_001163941.2:c.2010+1162C>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.2010+1162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,112 control chromosomes in the GnomAD database, including 6,230 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 0.26 (6230 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.2010+1162C>T		intron_variant	Intron 16 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.675+1162C>T		intron_variant	Intron 7 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.2010+1162C>T		intron_variant	Intron 16 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.675+1162C>T		intron_variant	Intron 7 of 18	1		ENSP00000258738.6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38787 AN: 151994 Hom.: 6205 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38848 AN: 152112 Hom.: 6230 Cov.: 32 AF XY: 0.249 AC XY: 18514 AN XY: 74382

African (AFR) AF: 0.448 AC: 18588 AN: 41452

American (AMR) AF: 0.239 AC: 3655 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 883 AN: 3470

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5186

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4812

European-Finnish (FIN) AF: 0.0727 AC: 771 AN: 10606

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12776 AN: 67992

Other (OTH) AF: 0.275 AC: 581 AN: 2112

Alfa AF: 0.215 Hom.: 6481

Bravo AF: 0.274

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-1.2
Mutation Taster		=100/0	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: rs17143258; hg19: chr7-20726621;