rs12334642

Positions:

• chr8-24384391-T-C

Variant summary

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

The NM_014479.3(ADAMDEC1):​c.-114T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0309 in 834,136 control chromosomes in the GnomAD database, including 509 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 0.036 (129 hom., cov: 32)
  • Exomes 𝑓: 0.030 (380 hom.)
• Consequence: ADAMDEC1 NM_014479.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

ADAMDEC1 (HGNC:16299): (ADAM like decysin 1) This encoded protein is thought to be a secreted protein belonging to the disintegrin metalloproteinase family. Its expression is upregulated during dendritic cells maturation. This protein may play an important role in dendritic cell function and their interactions with germinal center T cells. [provided by RefSeq, Jul 2008]

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMDEC1	NM_014479.3	c.-114T>C		5_prime_UTR_variant	1/14	ENST00000256412.8
ADAM7-AS1	NR_125808.1	n.501+2770A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMDEC1	ENST00000256412.8	c.-114T>C		5_prime_UTR_variant	1/14	1	NM_014479.3	P1
ADAM7-AS1	ENST00000519689.1	n.606+2770A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5470 AN: 152102 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0368

GnomAD4 exome AF: 0.0298 AC: 20341 AN: 681916 Hom.: 380 Cov.: 9 AF XY: 0.0299 AC XY: 10424 AN XY: 349200

Gnomad4 AFR exome AF: 0.0490

Gnomad4 AMR exome AF: 0.0254

Gnomad4 ASJ exome AF: 0.0260

Gnomad4 EAS exome AF: 0.0798

Gnomad4 SAS exome AF: 0.0330

Gnomad4 FIN exome AF: 0.0385

Gnomad4 NFE exome AF: 0.0253

Gnomad4 OTH exome AF: 0.0316

GnomAD4 genome AF: 0.0359 AC: 5467 AN: 152220 Hom.: 129 Cov.: 32 AF XY: 0.0359 AC XY: 2675 AN XY: 74412

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.0258

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.0683

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0292 Hom.: 87

Bravo AF: 0.0355

Asia WGS AF: 0.0590 AC: 205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12334642; hg19: chr8-24241904;