rs541688197
Positions:
- chr6-107635075-AGCCGCCGCC-A
- chr6-107635075-AGCCGCCGCC-AGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCCGCCGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCCGCCGCCGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCCGCCGCCGCCGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCCGCCGCCGCCGCCGCC
- chr6-107635075-AGCCGCCGCC-AGCCGCCGCCGCCGCCGCCGCCGCC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM4BP6_Very_StrongBS2
The NM_018013.4(SOBP):βc.2244_2252delβ(p.Pro749_Pro751del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000502 in 1,564,966 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.00044 ( 0 hom., cov: 31)
Exomes π: 0.00051 ( 3 hom. )
Consequence
SOBP
NM_018013.4 inframe_deletion
NM_018013.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.24
Genes affected
SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_018013.4.
BP6
?
Variant 6-107635075-AGCCGCCGCC-A is Benign according to our data. Variant chr6-107635075-AGCCGCCGCC-A is described in ClinVar as [Likely_benign]. Clinvar id is 1336256.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOBP | NM_018013.4 | c.2244_2252del | p.Pro749_Pro751del | inframe_deletion | 6/7 | ENST00000317357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOBP | ENST00000317357.10 | c.2244_2252del | p.Pro749_Pro751del | inframe_deletion | 6/7 | 5 | NM_018013.4 | P1 | |
SOBP | ENST00000494935.1 | n.99_107del | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000441 AC: 66AN: 149604Hom.: 0 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
66
AN:
149604
Hom.:
Cov.:
31
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:
GnomAD3 exomes AF: 0.00131 AC: 177AN: 135090Hom.: 0 AF XY: 0.00153 AC XY: 114AN XY: 74636
GnomAD3 exomes
AF:
AC:
177
AN:
135090
Hom.:
AF XY:
AC XY:
114
AN XY:
74636
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000508 AC: 719AN: 1415260Hom.: 3 AF XY: 0.000608 AC XY: 426AN XY: 700442
GnomAD4 exome
AF:
AC:
719
AN:
1415260
Hom.:
AF XY:
AC XY:
426
AN XY:
700442
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000441 AC: 66AN: 149706Hom.: 0 Cov.: 31 AF XY: 0.000452 AC XY: 33AN XY: 73046
GnomAD4 genome
?
AF:
AC:
66
AN:
149706
Hom.:
Cov.:
31
AF XY:
AC XY:
33
AN XY:
73046
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:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SOBP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 19, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 14, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at