rs2294426

chr6-11729849-A-Gchr6-11729849-A-T

Variant summary

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

The NM_032744.4(ADTRP):c.506+5719T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,142 control chromosomes in the GnomAD database, including 12,567 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 0.38 (12567 hom., cov: 32)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADTRP	NM_032744.4	c.506+5719T>C		intron_variant		ENST00000414691.8
LOC124901258	XR_007059452.1	n.251-209A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADTRP	ENST00000414691.8	c.506+5719T>C		intron_variant		1	NM_032744.4	P1
	ENST00000664082.1	n.468-209A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57080 AN: 152026 Hom.: 12562 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.375 AC: 57091 AN: 152142 Hom.: 12567 Cov.: 32 AF XY: 0.375 AC XY: 27869 AN XY: 74388

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.380

Alfa AF: 0.437 Hom.: 6586

Bravo AF: 0.364

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.3
Dann	Benign	0.69

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: rs2294426; hg19: chr6-11730082;