rs2291578

Positions:

• chr8-24399066-G-T

Variant summary

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

The NM_014479.3(ADAMDEC1):​c.929+26G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,600,238 control chromosomes in the GnomAD database, including 17,031 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 0.12 (1404 hom., cov: 32)
  • Exomes 𝑓: 0.14 (15627 hom.)
• Consequence: ADAMDEC1 NM_014479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3	c.929+26G>T		intron_variant		ENST00000256412.8	NP_055294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMDEC1	ENST00000256412.8	c.929+26G>T		intron_variant		1	NM_014479.3	ENSP00000256412.4

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17497 AN: 152042 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.122

GnomAD3 exomes AF: 0.151 AC: 36281 AN: 239652 Hom.: 3349 AF XY: 0.154 AC XY: 19974 AN XY: 129412

Gnomad AFR exome AF: 0.0353

Gnomad AMR exome AF: 0.152

Gnomad ASJ exome AF: 0.0730

Gnomad EAS exome AF: 0.378

Gnomad SAS exome AF: 0.181

Gnomad FIN exome AF: 0.147

Gnomad NFE exome AF: 0.132

Gnomad OTH exome AF: 0.130

GnomAD4 exome AF: 0.138 AC: 199852 AN: 1448078 Hom.: 15627 Cov.: 34 AF XY: 0.139 AC XY: 99894 AN XY: 719178

Gnomad4 AFR exome AF: 0.0307

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.0738

Gnomad4 EAS exome AF: 0.378

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.147

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.137

GnomAD4 genome AF: 0.115 AC: 17521 AN: 152160 Hom.: 1404 Cov.: 32 AF XY: 0.120 AC XY: 8943 AN XY: 74394

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.124

Alfa AF: 0.127 Hom.: 1885

Bravo AF: 0.112

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.43

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: rs2291578; hg19: chr8-24256579; COSMIC: COSV56475544;