6-11774559-C-T

Variant names:

• chr6-11774559-C-T
• rs6929400
• NM_032744.4:c.153+4048G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032744.4(ADTRP):​c.153+4048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,248 control chromosomes in the GnomAD database, including 38,022 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 0.70 (38022 hom., cov: 27)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.153+4048G>A		intron_variant	Intron 1 of 5	ENST00000414691.8	NP_116133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.153+4048G>A		intron_variant	Intron 1 of 5	1	NM_032744.4	ENSP00000404416.2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106200 AN: 151128 Hom.: 37974 Cov.: 27

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.703 AC: 106306 AN: 151248 Hom.: 38022 Cov.: 27 AF XY: 0.713 AC XY: 52661 AN XY: 73882

African (AFR) AF: 0.819 AC: 33750 AN: 41206

American (AMR) AF: 0.709 AC: 10759 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2180 AN: 3464

East Asian (EAS) AF: 0.917 AC: 4688 AN: 5110

South Asian (SAS) AF: 0.815 AC: 3888 AN: 4768

European-Finnish (FIN) AF: 0.705 AC: 7367 AN: 10456

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.611 AC: 41432 AN: 67766

Other (OTH) AF: 0.688 AC: 1448 AN: 2106

Alfa AF: 0.639 Hom.: 59347

Bravo AF: 0.705

Asia WGS AF: 0.854 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.53
PhyloP100		0.099
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: rs6929400; hg19: chr6-11774792;