rs12874914

Variant names:

• chr13-94744403-G-A
• rs12874914
• ENST00000665450.1:n.133-20005G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX21-AS1	ENST00000665450.1	n.133-20005G>A		intron_variant	Intron 1 of 3

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;