rs12334642
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_014479.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.34
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 -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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMDEC1 | NM_014479.3 | c.-114T>C | 5_prime_UTR_variant | 1/14 | ENST00000256412.8 | ||
ADAM7-AS1 | NR_125808.1 | n.501+2770A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMDEC1 | ENST00000256412.8 | c.-114T>C | 5_prime_UTR_variant | 1/14 | 1 | NM_014479.3 | P1 | ||
ADAM7-AS1 | ENST00000519689.1 | n.606+2770A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0360 AC: 5470AN: 152102Hom.: 129 Cov.: 32
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GnomAD4 exome AF: 0.0298 AC: 20341AN: 681916Hom.: 380 Cov.: 9 AF XY: 0.0299 AC XY: 10424AN XY: 349200
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GnomAD4 genome ? AF: 0.0359 AC: 5467AN: 152220Hom.: 129 Cov.: 32 AF XY: 0.0359 AC XY: 2675AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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