8-24879094-T-C

Position:

• chr8-24879094-T-C

Variant summary

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

The ENST00000519689.1(ADAM7-AS1):​n.184+4908A>G 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 0.131 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

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=-0.9).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.184+4908A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.139

Alfa AF: 0.113 Hom.: 977

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs196886; hg19: chr8-24736607;