chr7-20701544-C-T

Variant names:

• chr7-20701544-C-T
• rs4142216
• NM_001163941.2:c.2337+1409C>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.2337+1409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,910 control chromosomes in the GnomAD database, including 23,584 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 0.55 (23584 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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.2337+1409C>T		intron	N/A	NP_001157413.1
	ABCB5	NM_178559.6		c.1002+1409C>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.2337+1409C>T		intron	N/A	ENSP00000384881.2
	ABCB5	ENST00000258738.10	TSL:1	c.1002+1409C>T		intron	N/A	ENSP00000258738.6

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83457 AN: 151792 Hom.: 23576 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.550 AC: 83506 AN: 151910 Hom.: 23584 Cov.: 32 AF XY: 0.558 AC XY: 41458 AN XY: 74248

African (AFR) AF: 0.446 AC: 18450 AN: 41386

American (AMR) AF: 0.595 AC: 9076 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3468

East Asian (EAS) AF: 0.852 AC: 4415 AN: 5184

South Asian (SAS) AF: 0.710 AC: 3426 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6722 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37420 AN: 67928

Other (OTH) AF: 0.580 AC: 1221 AN: 2104

Alfa AF: 0.549 Hom.: 33896

Bravo AF: 0.542

Asia WGS AF: 0.758 AC: 2632 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.91
PhyloP100		0.61
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: rs4142216; hg19: chr7-20741167;