ENST00000519689.1:n.184+115223C>T

Variant names:

• chr8-24768779-G-A
• rs720517
• ENST00000519689.1:n.184+115223C>T

Variant summary

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

The ENST00000519689.1(ADAM7-AS1):​n.184+115223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,986 control chromosomes in the GnomAD database, including 2,183 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 0.17 (2183 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 6 publications found

Genes affected

ADAM7-AS1 (HGNC:56152): (ADAM7, ADAMDEC1 and ADAM28 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 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
ADAM7-AS1	ENST00000519689.1	n.184+115223C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25208 AN: 151870 Hom.: 2178 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.166 AC: 25237 AN: 151986 Hom.: 2183 Cov.: 32 AF XY: 0.169 AC XY: 12539 AN XY: 74302

African (AFR) AF: 0.192 AC: 7960 AN: 41450

American (AMR) AF: 0.115 AC: 1762 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.215 AC: 1103 AN: 5136

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4816

European-Finnish (FIN) AF: 0.171 AC: 1804 AN: 10556

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10037 AN: 67968

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.135 Hom.: 947

Bravo AF: 0.162

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs720517; hg19: chr8-24626292;