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rs5788775

chr10-126208852-GTTTTT-Gchr10-126208852-GTTTTT-GTTTchr10-126208852-GTTTTT-GTTTTchr10-126208852-GTTTTT-GTTTTTTchr10-126208852-GTTTTT-GTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTTTTTTTTTchr10-126208852-GTTTTT-GTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001288973.2(ADAM12):c.261-53552_261-53548del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 145,790 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 0)

Consequence

ADAM12
NM_001288973.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.457
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADAM12NM_001288973.2 linkuse as main transcriptc.261-53552_261-53548del intron_variant ENST00000448723.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADAM12ENST00000448723.2 linkuse as main transcriptc.261-53552_261-53548del intron_variant 5 NM_001288973.2 A2
ADAM12ENST00000368676.8 linkuse as main transcriptc.261-53552_261-53548del intron_variant 1 A2O43184-2
ADAM12ENST00000368679.8 linkuse as main transcriptc.261-53552_261-53548del intron_variant 1 P2O43184-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000117
AC:
17
AN:
145734
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000428
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000117
AC:
17
AN:
145790
Hom.:
0
Cov.:
0
AF XY:
0.0000708
AC XY:
5
AN XY:
70646
show subpopulations
Gnomad4 AFR
AF:
0.000427
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5788775; hg19: chr10-127897421; API