rs1015646

Variant names:

• chr7-20754097-T-A
• rs1015646
• NM_001163941.2:c.3576+591T>A

Variant summary

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

The NM_001163941.2(ABCB5):​c.3576+591T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,174 control chromosomes in the GnomAD database, including 13,810 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 0.41 (13810 hom., cov: 33)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.3576+591T>A		intron_variant	Intron 27 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.2241+591T>A		intron_variant	Intron 18 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.3576+591T>A		intron_variant	Intron 27 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.2241+591T>A		intron_variant	Intron 18 of 18	1		ENSP00000258738.6
ABCB5	ENST00000441315.1	n.930+8659T>A		intron_variant	Intron 6 of 7	2		ENSP00000398692.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62205 AN: 152054 Hom.: 13783 Cov.: 33

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.409 AC: 62286 AN: 152174 Hom.: 13810 Cov.: 33 AF XY: 0.402 AC XY: 29929 AN XY: 74388

African (AFR) AF: 0.590 AC: 24506 AN: 41510

American (AMR) AF: 0.314 AC: 4805 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5174

South Asian (SAS) AF: 0.274 AC: 1322 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3175 AN: 10600

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24598 AN: 67996

Other (OTH) AF: 0.375 AC: 793 AN: 2114

Alfa AF: 0.394 Hom.: 1578

Bravo AF: 0.419

Asia WGS AF: 0.248 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.73
PhyloP100		1.3
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: rs1015646; hg19: chr7-20793720;