rs4872262

Variant names:

• chr8-24768205-G-A
• rs4872262
• ENST00000519689.1:n.184+115797C>T

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+115797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,182 control chromosomes in the GnomAD database, including 488 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 0.060 (488 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519689.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM7-AS1	ENST00000519689.1	TSL:4	n.184+115797C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9099 AN: 152064 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0599 AC: 9117 AN: 152182 Hom.: 488 Cov.: 32 AF XY: 0.0610 AC XY: 4536 AN XY: 74388

African (AFR) AF: 0.120 AC: 4997 AN: 41516

American (AMR) AF: 0.0777 AC: 1188 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3472

East Asian (EAS) AF: 0.159 AC: 825 AN: 5178

South Asian (SAS) AF: 0.129 AC: 621 AN: 4818

European-Finnish (FIN) AF: 0.0234 AC: 248 AN: 10598

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1060 AN: 68000

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0305 Hom.: 744

Bravo AF: 0.0653

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4872262; hg19: chr8-24625718;