chr6-11779266-T-C

Variant names:

• chr6-11779266-T-C
• rs2076188
• ENST00000379415.6:c.-207-300A>G

Variant summary

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

The ENST00000379415.6(ADTRP):​c.-207-300A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,214 control chromosomes in the GnomAD database, including 32,972 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 0.63 (32941 hom., cov: 32)
  • Exomes 𝑓: 0.81 (31 hom.)
• Consequence: ADTRP ENST00000379415.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 6 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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.-207-300A>G		intron_variant	Intron 2 of 5	5		ENSP00000368726.2
ADTRP	ENST00000506810.1	c.-208+257A>G		intron_variant	Intron 1 of 4	3		ENSP00000422927.1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96435 AN: 152008 Hom.: 32931 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.635

GnomAD4 exome AF: 0.811 AC: 73 AN: 90 Hom.: 31 AF XY: 0.729 AC XY: 35 AN XY: 48

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.806 AC: 58 AN: 72

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.634 AC: 96470 AN: 152124 Hom.: 32941 Cov.: 32 AF XY: 0.628 AC XY: 46735 AN XY: 74400

African (AFR) AF: 0.386 AC: 15988 AN: 41470

American (AMR) AF: 0.713 AC: 10892 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2510 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2068 AN: 5180

South Asian (SAS) AF: 0.546 AC: 2629 AN: 4814

European-Finnish (FIN) AF: 0.744 AC: 7879 AN: 10594

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52195 AN: 67996

Other (OTH) AF: 0.637 AC: 1347 AN: 2114

Alfa AF: 0.718 Hom.: 143129

Bravo AF: 0.624

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.042
DANN	Benign	0.74
PhyloP100		-2.6
PromoterAI		0.072	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2076188; hg19: chr6-11779499;