7-20759446-G-T

Variant names:

• chr7-20759446-G-T
• rs17143334
• ENST00000441315.1:n.931-3810G>T

Variant summary

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

The ENST00000441315.1(ABCB5):​n.931-3810G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 152,216 control chromosomes in the GnomAD database, including 213 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 0.020 (213 hom., cov: 32)
• Consequence: ABCB5 ENST00000441315.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000441315.1	n.931-3810G>T		intron_variant	Intron 6 of 7	2		ENSP00000398692.1

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2975 AN: 152098 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.00237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00513

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0196 AC: 2988 AN: 152216 Hom.: 213 Cov.: 32 AF XY: 0.0223 AC XY: 1657 AN XY: 74430

Gnomad4 AFR AF: 0.00236

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.0347

Gnomad4 FIN AF: 0.0151

Gnomad4 NFE AF: 0.00513

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0117 Hom.: 12

Bravo AF: 0.0227

Asia WGS AF: 0.139 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17143334; hg19: chr7-20799069;