chr6-11774350-A-G

Position:

• chr6-11774350-A-G

Variant summary

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

The NM_032744.4(ADTRP):​c.153+4257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,694 control chromosomes in the GnomAD database, including 32,523 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 0.65 (32523 hom., cov: 29)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.153+4257T>C		intron_variant		ENST00000414691.8	NP_116133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.153+4257T>C		intron_variant		1	NM_032744.4	ENSP00000404416.2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98686 AN: 151578 Hom.: 32487 Cov.: 29

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.651 AC: 98778 AN: 151694 Hom.: 32523 Cov.: 29 AF XY: 0.661 AC XY: 48990 AN XY: 74118

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.649

Alfa AF: 0.632 Hom.: 63987

Bravo AF: 0.646

Asia WGS AF: 0.851 AC: 2955 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.76

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: rs6903956; hg19: chr6-11774583;