rs12674766

chr8-24384219-C-T

Variant summary

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

The NR_125808.1(ADAM7-AS1):n.501+2942G>A 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 0.374 in 356,086 control chromosomes in the GnomAD database, including 27,744 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 0.34 (10147 hom., cov: 32)
  • Exomes 𝑓: 0.40 (17597 hom.)
• Consequence: ADAM7-AS1 NR_125808.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAM7-AS1	NR_125808.1	n.501+2942G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAM7-AS1	ENST00000519689.1	n.606+2942G>A		intron_variant, non_coding_transcript_variant		4
ADAM7-AS1	ENST00000518988.5	n.355+2942G>A		intron_variant, non_coding_transcript_variant		2
ADAM7-AS1	ENST00000523578.5	n.501+2942G>A		intron_variant, non_coding_transcript_variant		4
ADAM7-AS1	ENST00000523700.5	n.164+2942G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51113 AN: 151830 Hom.: 10151 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.350

GnomAD4 exome AF: 0.402 AC: 82120 AN: 204136 Hom.: 17597 AF XY: 0.404 AC XY: 42301 AN XY: 104800

Gnomad4 AFR exome AF: 0.127

Gnomad4 AMR exome AF: 0.452

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.233

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.429

Gnomad4 NFE exome AF: 0.428

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.336 AC: 51105 AN: 151950 Hom.: 10147 Cov.: 32 AF XY: 0.338 AC XY: 25085 AN XY: 74240

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.346

Alfa AF: 0.371 Hom.: 1729

Bravo AF: 0.325

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.019
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: rs12674766; hg19: chr8-24241732;