rs196886

Variant names:

• chr8-24879094-T-C
• rs196886
• ENST00000519689.1:n.184+4908A>G

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+4908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,184 control chromosomes in the GnomAD database, including 1,602 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 0.13 (1602 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 5 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 = 0.386 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+4908A>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19979 AN: 152066 Hom.: 1598 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.131 AC: 20002 AN: 152184 Hom.: 1602 Cov.: 32 AF XY: 0.136 AC XY: 10137 AN XY: 74424

African (AFR) AF: 0.130 AC: 5413 AN: 41538

American (AMR) AF: 0.0872 AC: 1332 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2066 AN: 5164

South Asian (SAS) AF: 0.181 AC: 874 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1773 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7247 AN: 68004

Other (OTH) AF: 0.139 AC: 293 AN: 2114

Alfa AF: 0.112 Hom.: 1252

Bravo AF: 0.125

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs196886; hg19: chr8-24736607;