rs720517

Positions:

• chr8-24768779-G-A
• chr8-24768779-G-C

Variant summary

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

The ENST00000519689.1(ADAM7-AS1):​n.184+115223C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.184+115223C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.180

Alfa AF: 0.126 Hom.: 539

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720517; hg19: chr8-24626292;