6-154832777-TATAAG-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 6P and 2B. PVS1_StrongPM2BP6_Moderate
The NM_014892.5(SCAF8):c.3200_3204delTAAGA(p.Ile1067ArgfsTer20) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000684 in 1,461,844 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SCAF8
NM_014892.5 frameshift
NM_014892.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.97
Publications
0 publications found
Genes affected
SCAF8 (HGNC:20959): (SR-related CTD associated factor 8) Enables RNA binding activity and RNA polymerase II C-terminal domain phosphoserine binding activity. Involved in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled and positive regulation of DNA-templated transcription, elongation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
TIAM2 (HGNC:11806): (TIAM Rac1 associated GEF 2) This gene encodes a guanine nucleotide exchange factor. A highly similar mouse protein specifically activates ras-related C3 botulinum substrate 1, converting this Rho-like guanosine triphosphatase (GTPase) from a guanosine diphosphate-bound inactive state to a guanosine triphosphate-bound active state. The encoded protein may play a role in neural cell development. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.161 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-154832777-TATAAG-T is Benign according to our data. Variant chr6-154832777-TATAAG-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2429804.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014892.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SCAF8 | NM_014892.5 | MANE Select | c.3200_3204delTAAGA | p.Ile1067ArgfsTer20 | frameshift | Exon 20 of 20 | NP_055707.3 | ||
| SCAF8 | NM_001286188.1 | c.3434_3438delTAAGA | p.Ile1145ArgfsTer20 | frameshift | Exon 21 of 21 | NP_001273117.1 | Q9UPN6 | ||
| SCAF8 | NM_001286189.1 | c.3398_3402delTAAGA | p.Ile1133ArgfsTer20 | frameshift | Exon 22 of 22 | NP_001273118.1 | Q9UPN6-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SCAF8 | ENST00000367178.8 | TSL:2 MANE Select | c.3200_3204delTAAGA | p.Ile1067ArgfsTer20 | frameshift | Exon 20 of 20 | ENSP00000356146.3 | Q9UPN6-1 | |
| SCAF8 | ENST00000417268.3 | TSL:2 | c.3434_3438delTAAGA | p.Ile1145ArgfsTer20 | frameshift | Exon 21 of 21 | ENSP00000413098.2 | A0A0A0MT33 | |
| SCAF8 | ENST00000367186.7 | TSL:2 | c.3398_3402delTAAGA | p.Ile1133ArgfsTer20 | frameshift | Exon 22 of 22 | ENSP00000356154.4 | Q9UPN6-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461844Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 727222 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461844
Hom.:
AF XY:
AC XY:
0
AN XY:
727222
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39690
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53404
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111994
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
0.40
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0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Autism spectrum disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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