chr7-120787523-CAT-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_012338.4(TSPAN12):c.*1067_*1068del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 152,632 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 0 hom. )
Consequence
TSPAN12
NM_012338.4 3_prime_UTR
NM_012338.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.493
Genes affected
TSPAN12 (HGNC:21641): (tetraspanin 12) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 7-120787523-CAT-C is Benign according to our data. Variant chr7-120787523-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 358754.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0013 (198/152204) while in subpopulation AFR AF= 0.00323 (134/41550). AF 95% confidence interval is 0.00278. There are 0 homozygotes in gnomad4. There are 102 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN12 | NM_012338.4 | c.*1067_*1068del | 3_prime_UTR_variant | 8/8 | ENST00000222747.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN12 | ENST00000222747.8 | c.*1067_*1068del | 3_prime_UTR_variant | 8/8 | 1 | NM_012338.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00130 AC: 198AN: 152086Hom.: 0 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
198
AN:
152086
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00234 AC: 1AN: 428Hom.: 0 AF XY: 0.00388 AC XY: 1AN XY: 258
GnomAD4 exome
AF:
AC:
1
AN:
428
Hom.:
AF XY:
AC XY:
1
AN XY:
258
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00130 AC: 198AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00137 AC XY: 102AN XY: 74404
GnomAD4 genome
?
AF:
AC:
198
AN:
152204
Hom.:
Cov.:
33
AF XY:
AC XY:
102
AN XY:
74404
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3468
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial exudative vitreoretinopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at