chr8-24393296-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014479.3(ADAMDEC1):c.242T>C(p.Ile81Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00436 in 1,605,972 control chromosomes in the GnomAD database, including 279 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 135 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 144 hom. )
Consequence
ADAMDEC1
NM_014479.3 missense
NM_014479.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -3.04
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0026058555).
BP6
?
Variant 8-24393296-T-C is Benign according to our data. Variant chr8-24393296-T-C is described in ClinVar as [Benign]. Clinvar id is 781120.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMDEC1 | NM_014479.3 | c.242T>C | p.Ile81Thr | missense_variant | 3/14 | ENST00000256412.8 | |
ADAM7-AS1 | NR_125808.1 | n.80-5305A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMDEC1 | ENST00000256412.8 | c.242T>C | p.Ile81Thr | missense_variant | 3/14 | 1 | NM_014479.3 | P1 | |
ADAM7-AS1 | ENST00000519689.1 | n.185-5305A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0236 AC: 3588AN: 152088Hom.: 134 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00597 AC: 1475AN: 247076Hom.: 65 AF XY: 0.00433 AC XY: 578AN XY: 133532
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GnomAD4 exome AF: 0.00234 AC: 3399AN: 1453766Hom.: 144 Cov.: 28 AF XY: 0.00195 AC XY: 1410AN XY: 723270
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GnomAD4 genome ? AF: 0.0237 AC: 3605AN: 152206Hom.: 135 Cov.: 32 AF XY: 0.0228 AC XY: 1698AN XY: 74432
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903
Asia WGS
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3470
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at