rs78414512

chr7-20628654-C-A

Variant summary

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

The NM_001163941.2(ABCB5):c.109-34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,590,304 control chromosomes in the GnomAD database, including 16,061 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 0.11 (1208 hom., cov: 32)
  • Exomes 𝑓: 0.14 (14853 hom.)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB5	NM_001163941.2	c.109-34C>A		intron_variant		ENST00000404938.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB5	ENST00000404938.7	c.109-34C>A		intron_variant		1	NM_001163941.2	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16516 AN: 151010 Hom.: 1208 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.000788

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.0976

GnomAD3 exomes AF: 0.113 AC: 25715 AN: 226808 Hom.: 1895 AF XY: 0.116 AC XY: 14210 AN XY: 122518

Gnomad AFR exome AF: 0.0214

Gnomad AMR exome AF: 0.0624

Gnomad ASJ exome AF: 0.124

Gnomad EAS exome AF: 0.00191

Gnomad SAS exome AF: 0.0692

Gnomad FIN exome AF: 0.223

Gnomad NFE exome AF: 0.150

Gnomad OTH exome AF: 0.124

GnomAD4 exome AF: 0.137 AC: 197309 AN: 1439172 Hom.: 14853 Cov.: 31 AF XY: 0.136 AC XY: 96967 AN XY: 713988

Gnomad4 AFR exome AF: 0.0187

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.127

Gnomad4 EAS exome AF: 0.00108

Gnomad4 SAS exome AF: 0.0704

Gnomad4 FIN exome AF: 0.222

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.109 AC: 16515 AN: 151132 Hom.: 1208 Cov.: 32 AF XY: 0.111 AC XY: 8199 AN XY: 73832

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.000790

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.133 Hom.: 300

Bravo AF: 0.0950

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.050
Dann	Benign	0.52

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: rs78414512; hg19: chr7-20668277;