rs73076550

chr7-20615769-C-T

Variant summary

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

The NM_001163941.2(ABCB5):c.-90C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 152,290 control chromosomes in the GnomAD database, including 777 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 0.099 (777 hom., cov: 32)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: ABCB5 NM_001163941.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB5	NM_001163941.2	c.-90C>T		5_prime_UTR_variant	1/28	ENST00000404938.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB5	ENST00000404938.7	c.-90C>T		5_prime_UTR_variant	1/28	1	NM_001163941.2	P1

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14989 AN: 152042 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0799

GnomAD4 exome AF: 0.108 AC: 14 AN: 130 Hom.: 0 Cov.: 0 AF XY: 0.0811 AC XY: 6 AN XY: 74

Gnomad4 EAS exome AF: 0.114

Gnomad4 NFE exome AF: 0.0625

GnomAD4 genome AF: 0.0986 AC: 14998 AN: 152160 Hom.: 777 Cov.: 32 AF XY: 0.0968 AC XY: 7199 AN XY: 74376

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0961 Hom.: 434

Bravo AF: 0.103

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.9
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs73076550; hg19: chr7-20655392;