rs12334642

Variant names:

• chr8-24384391-T-C
• rs12334642
• NM_014479.3:c.-114T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3	c.-114T>C		5_prime_UTR_variant	Exon 1 of 14	ENST00000256412.8	NP_055294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMDEC1	ENST00000256412.8	c.-114T>C		5_prime_UTR_variant	Exon 1 of 14	1	NM_014479.3	ENSP00000256412.4

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

African (AFR) AF: 0.0490 AC: 759 AN: 15484

American (AMR) AF: 0.0254 AC: 433 AN: 17066

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 386 AN: 14862

East Asian (EAS) AF: 0.0798 AC: 2393 AN: 29982

South Asian (SAS) AF: 0.0330 AC: 1613 AN: 48828

European-Finnish (FIN) AF: 0.0385 AC: 1442 AN: 37460

Middle Eastern (MID) AF: 0.0202 AC: 81 AN: 4018

European-Non Finnish (NFE) AF: 0.0253 AC: 12181 AN: 480896

Other (OTH) AF: 0.0316 AC: 1053 AN: 33320

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

African (AFR) AF: 0.0499 AC: 2072 AN: 41550

American (AMR) AF: 0.0258 AC: 395 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 353 AN: 5166

South Asian (SAS) AF: 0.0392 AC: 189 AN: 4824

European-Finnish (FIN) AF: 0.0364 AC: 386 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1807 AN: 67992

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0299 Hom.: 110

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
PhyloP100		-1.3
PromoterAI		-0.017	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12334642; hg19: chr8-24241904;