rs16933090
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000396356.7(SOX6):c.-5+42068G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,992 control chromosomes in the GnomAD database, including 1,159 homozygotes. 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: 𝑓 0.12 ( 1159 hom., cov: 32)
Exomes 𝑓: 0.13 ( 0 hom. )
Consequence
SOX6
ENST00000396356.7 intron
ENST00000396356.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.06
Genes affected
SOX6 (HGNC:16421): (SRY-box transcription factor 6) This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX6 | NM_001367872.1 | c.-4-92995G>A | intron_variant | ||||
SOX6 | NM_033326.3 | c.-5+42068G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX6 | ENST00000396356.7 | c.-5+42068G>A | intron_variant | 1 | P4 | ||||
SOX6 | ENST00000529469.1 | c.-108G>A | 5_prime_UTR_variant | 1/2 | 4 | ||||
SOX6 | ENST00000530378.5 | c.-5+42068G>A | intron_variant, NMD_transcript_variant | 2 | |||||
SOX6 | ENST00000533658.5 | n.333+31454G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17827AN: 151866Hom.: 1155 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
17827
AN:
151866
Hom.:
Cov.:
32
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: 0.125 AC: 1AN: 8Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1AN XY: 6
GnomAD4 exome
AF:
AC:
1
AN:
8
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
6
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.117 AC: 17852AN: 151984Hom.: 1159 Cov.: 32 AF XY: 0.115 AC XY: 8561AN XY: 74252
GnomAD4 genome
?
AF:
AC:
17852
AN:
151984
Hom.:
Cov.:
32
AF XY:
AC XY:
8561
AN XY:
74252
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:
192
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at