NM_001163941.2:c.-90C>T

Variant names:

• chr7-20615769-C-T
• rs73076550
• NM_001163941.2:c.-90C>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.-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
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	NM_001163941.2	MANE Select	c.-90C>T		5_prime_UTR	Exon 1 of 28	NP_001157413.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.-90C>T		5_prime_UTR	Exon 1 of 28	ENSP00000384881.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.114 AC: 13 AN: 114

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0625 AC: 1 AN: 16

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.104 AC: 4325 AN: 41504

American (AMR) AF: 0.119 AC: 1821 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.155 AC: 802 AN: 5172

South Asian (SAS) AF: 0.0877 AC: 422 AN: 4814

European-Finnish (FIN) AF: 0.0606 AC: 642 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6492 AN: 67994

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0969 Hom.: 1396

Bravo AF: 0.103

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		0.26
PromoterAI		-0.0098	Neutral
Mutation Taster		=299/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs73076550; hg19: chr7-20655392;