rs7305773

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000451604.7(SOX5):​c.481+27731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,198 control chromosomes in the GnomAD database, including 1,139 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 0.11 ( 1139 hom., cov: 32)

Consequence

SOX5
ENST00000451604.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.425
Variant links:
Genes affected
SOX5 (HGNC:11201): (SRY-box transcription factor 5) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SOX5NM_006940.6 linkuse as main transcriptc.481+27731A>G intron_variant ENST00000451604.7 NP_008871.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SOX5ENST00000451604.7 linkuse as main transcriptc.481+27731A>G intron_variant 1 NM_006940.6 ENSP00000398273 A1P35711-1

Frequencies

GnomAD3 genomes
AF:
0.115
AC:
17444
AN:
152080
Hom.:
1136
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0766
Gnomad AMI
AF:
0.133
Gnomad AMR
AF:
0.0715
Gnomad ASJ
AF:
0.103
Gnomad EAS
AF:
0.00193
Gnomad SAS
AF:
0.0976
Gnomad FIN
AF:
0.152
Gnomad MID
AF:
0.118
Gnomad NFE
AF:
0.153
Gnomad OTH
AF:
0.0976
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.115
AC:
17457
AN:
152198
Hom.:
1139
Cov.:
32
AF XY:
0.115
AC XY:
8523
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.0769
Gnomad4 AMR
AF:
0.0713
Gnomad4 ASJ
AF:
0.103
Gnomad4 EAS
AF:
0.00193
Gnomad4 SAS
AF:
0.0972
Gnomad4 FIN
AF:
0.152
Gnomad4 NFE
AF:
0.153
Gnomad4 OTH
AF:
0.0966
Alfa
AF:
0.142
Hom.:
2135
Bravo
AF:
0.106
Asia WGS
AF:
0.0430
AC:
152
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.4
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs7305773; hg19: chr12-23971186; API