rs2245371

chr8-24784872-A-G

Variant summary

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

The ENST00000519689.1(ADAM7-AS1):n.184+99130T>C 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 0.206 in 149,322 control chromosomes in the GnomAD database, including 3,810 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 0.21 (3810 hom., cov: 30)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.184+99130T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 30735 AN: 149246 Hom.: 3806 Cov.: 30

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.00473

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.206 AC: 30768 AN: 149322 Hom.: 3810 Cov.: 30 AF XY: 0.201 AC XY: 14633 AN XY: 72778

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.00474

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.183

Alfa AF: 0.200 Hom.: 410

Bravo AF: 0.208

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0070
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245371; hg19: chr8-24642385;