7-20724284-C-T

Variant names:

• chr7-20724284-C-T
• rs6461513
• NM_001163941.2:c.2625+1065C>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.2625+1065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 151,418 control chromosomes in the GnomAD database, including 42,759 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 0.75 (42759 hom., cov: 27)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.2625+1065C>T		intron_variant	Intron 21 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.1290+1065C>T		intron_variant	Intron 12 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.2625+1065C>T		intron_variant	Intron 21 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.1290+1065C>T		intron_variant	Intron 12 of 18	1		ENSP00000258738.6
ABCB5	ENST00000441315.1	n.126+1065C>T		intron_variant	Intron 1 of 7	2		ENSP00000398692.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 112977 AN: 151298 Hom.: 42715 Cov.: 27

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.747 AC: 113083 AN: 151418 Hom.: 42759 Cov.: 27 AF XY: 0.747 AC XY: 55180 AN XY: 73910

African (AFR) AF: 0.846 AC: 34910 AN: 41250

American (AMR) AF: 0.775 AC: 11790 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2652 AN: 3460

East Asian (EAS) AF: 0.922 AC: 4752 AN: 5152

South Asian (SAS) AF: 0.713 AC: 3404 AN: 4776

European-Finnish (FIN) AF: 0.621 AC: 6441 AN: 10372

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46664 AN: 67894

Other (OTH) AF: 0.761 AC: 1597 AN: 2098

Alfa AF: 0.707 Hom.: 67939

Bravo AF: 0.766

Asia WGS AF: 0.826 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.68
PhyloP100		-0.16
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: rs6461513; hg19: chr7-20763907;