chr7-20639663-G-A

Position:

• chr7-20639663-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001163941.2(ABCB5):​c.315-3521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,068 control chromosomes in the GnomAD database, including 7,261 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 0.27 (7261 hom., cov: 33)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB5	NM_001163941.2	c.315-3521G>A		intron_variant		ENST00000404938.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB5	ENST00000404938.7	c.315-3521G>A		intron_variant		1	NM_001163941.2	P1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41187 AN: 151950 Hom.: 7248 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.271 AC: 41246 AN: 152068 Hom.: 7261 Cov.: 33 AF XY: 0.269 AC XY: 20006 AN XY: 74334

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.234

Alfa AF: 0.188 Hom.: 4146

Bravo AF: 0.284

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188594; hg19: chr7-20679286;