NM_014479.3:c.846C>T

Variant names:

• chr8-24398957-C-T
• rs2291577
• NM_014479.3:c.846C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_014479.3(ADAMDEC1):​c.846C>T​(p.Ser282Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 1,613,164 control chromosomes in the GnomAD database, including 142,531 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 (10219 hom., cov: 31)
  • Exomes 𝑓: 0.42 (132312 hom.)
• Consequence: ADAMDEC1 NM_014479.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP7: Synonymous conserved (PhyloP=-2.22 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3	c.846C>T	p.Ser282Ser	synonymous_variant	Exon 9 of 14	ENST00000256412.8	NP_055294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMDEC1	ENST00000256412.8	c.846C>T	p.Ser282Ser	synonymous_variant	Exon 9 of 14	1	NM_014479.3	ENSP00000256412.4

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51830 AN: 151768 Hom.: 10223 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.352

GnomAD3 exomes AF: 0.400 AC: 100264 AN: 250552 Hom.: 21442 AF XY: 0.406 AC XY: 54933 AN XY: 135436

Gnomad AFR exome AF: 0.135

Gnomad AMR exome AF: 0.466

Gnomad ASJ exome AF: 0.505

Gnomad EAS exome AF: 0.191

Gnomad SAS exome AF: 0.426

Gnomad FIN exome AF: 0.425

Gnomad NFE exome AF: 0.429

Gnomad OTH exome AF: 0.423

GnomAD4 exome AF: 0.420 AC: 614149 AN: 1461278 Hom.: 132312 Cov.: 46 AF XY: 0.422 AC XY: 306842 AN XY: 726968

Gnomad4 AFR exome AF: 0.131

Gnomad4 AMR exome AF: 0.464

Gnomad4 ASJ exome AF: 0.503

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.433

Gnomad4 OTH exome AF: 0.401

GnomAD4 genome AF: 0.341 AC: 51823 AN: 151886 Hom.: 10219 Cov.: 31 AF XY: 0.343 AC XY: 25423 AN XY: 74226

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.347

Alfa AF: 0.385 Hom.: 7730

Bravo AF: 0.331

Asia WGS AF: 0.308 AC: 1072 AN: 3478

EpiCase AF: 0.418

EpiControl AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.32
DANN	Benign	0.50

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: rs2291577; hg19: chr8-24256470; COSMIC: COSV56475384;