6-11729849-A-G

Variant names:

• chr6-11729849-A-G
• rs2294426
• NM_032744.4:c.506+5719T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ENSG00000287593 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032744.4. 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
	ADTRP	NM_032744.4	MANE Select	c.506+5719T>C		intron	N/A	NP_116133.1
	ADTRP	NM_001143948.2		c.560+5719T>C		intron	N/A	NP_001137420.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADTRP	ENST00000414691.8	TSL:1 MANE Select	c.506+5719T>C		intron	N/A	ENSP00000404416.2
	ADTRP	ENST00000229583.9	TSL:2	c.560+5719T>C		intron	N/A	ENSP00000229583.5
	ADTRP	ENST00000503285.1	TSL:5	c.89+5719T>C		intron	N/A	ENSP00000426507.1

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

African (AFR) AF: 0.150 AC: 6207 AN: 41504

American (AMR) AF: 0.387 AC: 5919 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3466

East Asian (EAS) AF: 0.716 AC: 3708 AN: 5178

South Asian (SAS) AF: 0.436 AC: 2104 AN: 4824

European-Finnish (FIN) AF: 0.418 AC: 4425 AN: 10574

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.467 AC: 31773 AN: 67996

Other (OTH) AF: 0.380 AC: 803 AN: 2114

Alfa AF: 0.434 Hom.: 27741

Bravo AF: 0.364

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		0.019
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2294426; hg19: chr6-11730082;