chr7-20747650-C-T

Variant names:

• chr7-20747650-C-T
• rs6461517
• NM_001163941.2:c.3429+2212C>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.3429+2212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,064 control chromosomes in the GnomAD database, including 9,439 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 0.35 (9439 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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.3429+2212C>T		intron	N/A	NP_001157413.1	Q2M3G0-4
	ABCB5	NM_178559.6		c.2094+2212C>T		intron	N/A	NP_848654.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.3429+2212C>T		intron	N/A	ENSP00000384881.2	Q2M3G0-4
	ABCB5	ENST00000258738.10	TSL:1	c.2094+2212C>T		intron	N/A	ENSP00000258738.6	Q2M3G0-1
	ABCB5	ENST00000441315.1	TSL:2	n.930+2212C>T		intron	N/A	ENSP00000398692.1	H7C165

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53048 AN: 151944 Hom.: 9428 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.349 AC: 53096 AN: 152064 Hom.: 9439 Cov.: 32 AF XY: 0.342 AC XY: 25385 AN XY: 74326

African (AFR) AF: 0.387 AC: 16055 AN: 41478

American (AMR) AF: 0.291 AC: 4448 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1069 AN: 5182

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4814

European-Finnish (FIN) AF: 0.269 AC: 2841 AN: 10552

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24595 AN: 67976

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.358 Hom.: 8062

Bravo AF: 0.352

Asia WGS AF: 0.235 AC: 821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.21
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: rs6461517; hg19: chr7-20787273;