rs2245371

Variant names:

• chr8-24784872-A-G
• rs2245371
• ENST00000519689.1:n.184+99130T>C

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+99130T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 1 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=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.184+99130T>C		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.351 AC: 14289 AN: 40668

American (AMR) AF: 0.117 AC: 1759 AN: 15008

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 559 AN: 3438

East Asian (EAS) AF: 0.00474 AC: 24 AN: 5058

South Asian (SAS) AF: 0.111 AC: 521 AN: 4698

European-Finnish (FIN) AF: 0.165 AC: 1619 AN: 9824

Middle Eastern (MID) AF: 0.180 AC: 51 AN: 284

European-Non Finnish (NFE) AF: 0.169 AC: 11419 AN: 67378

Other (OTH) AF: 0.183 AC: 378 AN: 2062

Alfa AF: 0.205 Hom.: 451

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
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2245371; hg19: chr8-24642385;