rs7311001

Variant summary

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

The NM_006940.6(SOX5):​c.1018-5715T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,938 control chromosomes in the GnomAD database, including 7,287 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 0.31 ( 7287 hom., cov: 32)

Consequence

SOX5
NM_006940.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.322
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=-0.66).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SOX5NM_006940.6 linkuse as main transcriptc.1018-5715T>A intron_variant ENST00000451604.7 NP_008871.3 P35711-1A0A024RB06

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SOX5ENST00000451604.7 linkuse as main transcriptc.1018-5715T>A intron_variant 1 NM_006940.6 ENSP00000398273.2 P35711-1

Frequencies

GnomAD3 genomes
AF:
0.306
AC:
46423
AN:
151820
Hom.:
7284
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.313
Gnomad AMI
AF:
0.535
Gnomad AMR
AF:
0.260
Gnomad ASJ
AF:
0.453
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.318
Gnomad FIN
AF:
0.275
Gnomad MID
AF:
0.360
Gnomad NFE
AF:
0.304
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.306
AC:
46463
AN:
151938
Hom.:
7287
Cov.:
32
AF XY:
0.306
AC XY:
22715
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.313
Gnomad4 AMR
AF:
0.260
Gnomad4 ASJ
AF:
0.453
Gnomad4 EAS
AF:
0.314
Gnomad4 SAS
AF:
0.317
Gnomad4 FIN
AF:
0.275
Gnomad4 NFE
AF:
0.304
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.291
Hom.:
837
Bravo
AF:
0.303
Asia WGS
AF:
0.360
AC:
1252
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
9.5
DANN
Benign
0.92

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: rs7311001; hg19: chr12-23763182; API