rs1018383

Variant names:

• chr6-11784092-C-T
• rs1018383
• ENST00000379415.6:c.-207-5126G>A

Variant summary

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

The ENST00000379415.6(ADTRP):​c.-207-5126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 151,806 control chromosomes in the GnomAD database, including 44,455 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 0.76 (44455 hom., cov: 29)
• Consequence: ADTRP ENST00000379415.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

ADTRP (HGNC:21214): (androgen dependent TFPI regulating protein) Enables hydrolase activity. Involved in several processes, including cell migration involved in sprouting angiogenesis; negative regulation of secretion by cell; and positive regulation of macromolecule metabolic process. Located in caveola and cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 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
ADTRP	ENST00000379415.6	c.-207-5126G>A		intron_variant	Intron 2 of 5	5		ENSP00000368726.2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 114948 AN: 151690 Hom.: 44432 Cov.: 29

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.758 AC: 115011 AN: 151806 Hom.: 44455 Cov.: 29 AF XY: 0.754 AC XY: 55962 AN XY: 74190

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.750

Alfa AF: 0.806 Hom.: 6193

Bravo AF: 0.745

Asia WGS AF: 0.587 AC: 2039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.78
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018383; hg19: chr6-11784325;