rs1013209

Variant names:

• chr8-24258791-C-T
• rs1013209
• ENST00000521681.3:n.321+37363G>A

Variant summary

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

The ENST00000521681.3(ADAM7-AS1):​n.321+37363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,862 control chromosomes in the GnomAD database, including 5,978 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 0.28 (5978 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000521681.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 27 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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	ENST00000521681.3	n.321+37363G>A		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41731 AN: 151746 Hom.: 5960 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.275 AC: 41793 AN: 151862 Hom.: 5978 Cov.: 32 AF XY: 0.280 AC XY: 20809 AN XY: 74214

African (AFR) AF: 0.301 AC: 12460 AN: 41392

American (AMR) AF: 0.329 AC: 5007 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3468

East Asian (EAS) AF: 0.338 AC: 1740 AN: 5152

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4826

European-Finnish (FIN) AF: 0.321 AC: 3378 AN: 10530

Middle Eastern (MID) AF: 0.169 AC: 49 AN: 290

European-Non Finnish (NFE) AF: 0.241 AC: 16346 AN: 67958

Other (OTH) AF: 0.251 AC: 531 AN: 2112

Alfa AF: 0.254 Hom.: 15009

Bravo AF: 0.275

Asia WGS AF: 0.290 AC: 1004 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.46
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1013209; hg19: chr8-24116304;