GeneBe

NM_001288973.2:c.260+5882C>G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001288973.2(ADAM12):​c.260+5882C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ADAM12
NM_001288973.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

1 publications found
Variant links:
Genes affected
ADAM12 (HGNC:190): (ADAM metallopeptidase domain 12) This gene encodes a member of a family of proteins that are structurally related to snake venom disintegrins and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. Expression of this gene has been used as a maternal serum marker for pre-natal development. Alternative splicing results in multiple transcript variants encoding different isoforms. Shorter isoforms are secreted, while longer isoforms are membrane-bound form. [provided by RefSeq, Jan 2014]
SAR1AP2 (HGNC:20770): (secretion associated Ras related GTPase 1A pseudogene 2)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADAM12NM_001288973.2 linkc.260+5882C>G intron_variant Intron 3 of 22 ENST00000448723.2 NP_001275902.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADAM12ENST00000448723.2 linkc.260+5882C>G intron_variant Intron 3 of 22 5 NM_001288973.2 ENSP00000391268.2 Q5JRP2
ADAM12ENST00000368679.8 linkc.260+5882C>G intron_variant Intron 3 of 22 1 ENSP00000357668.4 O43184-1
ADAM12ENST00000368676.8 linkc.260+5882C>G intron_variant Intron 3 of 18 1 ENSP00000357665.4 O43184-2
SAR1AP2ENST00000392696.2 linkn.216G>C non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1624
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
954
African (AFR)
AF:
0.00
AC:
0
AN:
48
American (AMR)
AF:
0.00
AC:
0
AN:
102
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
38
East Asian (EAS)
AF:
0.00
AC:
0
AN:
48
South Asian (SAS)
AF:
0.00
AC:
0
AN:
318
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
96
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
6
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
854
Other (OTH)
AF:
0.00
AC:
0
AN:
114
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
0.99
DANN
Benign
0.46
PhyloP100
-0.23

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

Other links and lift over

dbSNP: rs7095359; hg19: chr10-127961602; API