rs17218839

Variant names:

• chr7-20705795-G-A
• rs17218839
• NM_001163941.2:c.2421+988G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-20705795-G-A
• chr7-20705795-G-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.2421+988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 150,608 control chromosomes in the GnomAD database, including 4,402 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 0.23 (4402 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.2421+988G>A		intron_variant	Intron 20 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.1086+988G>A		intron_variant	Intron 11 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.2421+988G>A		intron_variant	Intron 20 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.1086+988G>A		intron_variant	Intron 11 of 18	1		ENSP00000258738.6

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35056 AN: 150502 Hom.: 4401 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.233 AC: 35077 AN: 150608 Hom.: 4402 Cov.: 32 AF XY: 0.229 AC XY: 16814 AN XY: 73544

African (AFR) AF: 0.196 AC: 8003 AN: 40780

American (AMR) AF: 0.246 AC: 3727 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3470

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5164

South Asian (SAS) AF: 0.162 AC: 776 AN: 4794

European-Finnish (FIN) AF: 0.211 AC: 2155 AN: 10212

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18650 AN: 67758

Other (OTH) AF: 0.242 AC: 505 AN: 2090

Alfa AF: 0.197 Hom.: 740

Bravo AF: 0.233

Asia WGS AF: 0.100 AC: 348 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.19
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: rs17218839; hg19: chr7-20745418; COSMIC: COSV51706737;