ENST00000519689.1:n.185-229114A>G

Variant names:

• chr8-24617105-T-C
• rs10503756
• ENST00000519689.1:n.185-229114A>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.185-229114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,302 control chromosomes in the GnomAD database, including 260 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 0.044 (260 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000519689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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.185-229114A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6652 AN: 152184 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0438 AC: 6666 AN: 152302 Hom.: 260 Cov.: 32 AF XY: 0.0444 AC XY: 3310 AN XY: 74480

African (AFR) AF: 0.0851 AC: 3538 AN: 41560

American (AMR) AF: 0.0639 AC: 978 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.142 AC: 737 AN: 5178

South Asian (SAS) AF: 0.0627 AC: 303 AN: 4830

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10628

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 955 AN: 68016

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0293 Hom.: 19

Bravo AF: 0.0508

Asia WGS AF: 0.111 AC: 384 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		-0.41
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: rs10503756; hg19: chr8-24474618;