chr8-24248249-G-T

Variant names:

• chr8-24248249-G-T
• rs17051743
• ENST00000521681.3:n.321+47905C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521681.3(ADAM7-AS1):​n.321+47905C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,858 control chromosomes in the GnomAD database, including 8,107 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 0.32 (8107 hom., cov: 32)
• Consequence: ADAM7-AS1 ENST00000521681.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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	ENST00000521681.3	n.321+47905C>A		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48649 AN: 151736 Hom.: 8091 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.321 AC: 48701 AN: 151858 Hom.: 8107 Cov.: 32 AF XY: 0.326 AC XY: 24221 AN XY: 74212

African (AFR) AF: 0.372 AC: 15402 AN: 41434

American (AMR) AF: 0.357 AC: 5440 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3464

East Asian (EAS) AF: 0.401 AC: 2061 AN: 5134

South Asian (SAS) AF: 0.377 AC: 1817 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3464 AN: 10536

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18568 AN: 67916

Other (OTH) AF: 0.285 AC: 602 AN: 2110

Alfa AF: 0.284 Hom.: 19520

Bravo AF: 0.319

Asia WGS AF: 0.404 AC: 1404 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	0.21
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17051743; hg19: chr8-24105762;