rs12874914

chr13-94744403-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665450.1(SOX21-AS1):n.133-20005G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,908 control chromosomes in the GnomAD database, including 3,362 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 0.20 (3362 hom., cov: 31)
• Consequence: SOX21-AS1 ENST00000665450.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

SOX21-AS1 (HGNC:39807): (SOX21 antisense divergent transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX21-AS1	ENST00000665450.1	n.133-20005G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29841 AN: 151790 Hom.: 3361 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29849 AN: 151908 Hom.: 3362 Cov.: 31 AF XY: 0.200 AC XY: 14845 AN XY: 74202

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.196

Alfa AF: 0.201 Hom.: 418

Bravo AF: 0.186

Asia WGS AF: 0.369 AC: 1281 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	0.88
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12874914; hg19: chr13-95396657;