rs10087305

Variant names:

• chr8-24384460-G-C
• rs10087305
• NM_014479.3:c.-45G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-24384460-G-C
• chr8-24384460-G-T

Variant summary

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

The NM_014479.3(ADAMDEC1):​c.-45G>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 0.138 in 1,465,818 control chromosomes in the GnomAD database, including 15,878 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 0.14 (1782 hom., cov: 33)
  • Exomes 𝑓: 0.14 (14096 hom.)
• Consequence: ADAMDEC1 NM_014479.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3	c.-45G>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.-45G>C		5_prime_UTR_variant	Exon 1 of 14	1	NM_014479.3	ENSP00000256412.4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21877 AN: 151900 Hom.: 1779 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.140

GnomAD2 exomes AF: 0.155 AC: 23788 AN: 153364 AF XY: 0.156

Gnomad AFR exome AF: 0.155

Gnomad AMR exome AF: 0.158

Gnomad ASJ exome AF: 0.0697

Gnomad EAS exome AF: 0.387

Gnomad FIN exome AF: 0.132

Gnomad NFE exome AF: 0.125

Gnomad OTH exome AF: 0.121

GnomAD4 exome AF: 0.137 AC: 179749 AN: 1313800 Hom.: 14096 Cov.: 18 AF XY: 0.137 AC XY: 89287 AN XY: 650702

African (AFR) AF: 0.149 AC: 4217 AN: 28362

American (AMR) AF: 0.152 AC: 4348 AN: 28528

Ashkenazi Jewish (ASJ) AF: 0.0693 AC: 1559 AN: 22482

East Asian (EAS) AF: 0.388 AC: 13901 AN: 35822

South Asian (SAS) AF: 0.168 AC: 12381 AN: 73750

European-Finnish (FIN) AF: 0.128 AC: 6422 AN: 50208

Middle Eastern (MID) AF: 0.125 AC: 668 AN: 5340

European-Non Finnish (NFE) AF: 0.127 AC: 128578 AN: 1014772

Other (OTH) AF: 0.141 AC: 7675 AN: 54536

GnomAD4 genome AF: 0.144 AC: 21907 AN: 152018 Hom.: 1782 Cov.: 33 AF XY: 0.147 AC XY: 10959 AN XY: 74302

African (AFR) AF: 0.152 AC: 6310 AN: 41486

American (AMR) AF: 0.142 AC: 2167 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2033 AN: 5146

South Asian (SAS) AF: 0.187 AC: 903 AN: 4818

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10566

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8583 AN: 67952

Other (OTH) AF: 0.141 AC: 297 AN: 2104

Alfa AF: 0.119 Hom.: 229

Bravo AF: 0.147

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.54
PhyloP100		0.24
PromoterAI		-0.015	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: rs10087305; hg19: chr8-24241973; COSMIC: COSV56474452; COSMIC: COSV56474452;