chr13-94716585-A-G

Variant names:

• chr13-94716585-A-G
• rs9524596
• ENST00000665450.1:n.132+13000A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665450.1(SOX21-AS1):​n.132+13000A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,078 control chromosomes in the GnomAD database, including 11,080 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 0.38 (11080 hom., cov: 33)
• Consequence: SOX21-AS1 ENST00000665450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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.132+13000A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57124 AN: 151960 Hom.: 11081 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.376 AC: 57138 AN: 152078 Hom.: 11080 Cov.: 33 AF XY: 0.365 AC XY: 27172 AN XY: 74344

African (AFR) AF: 0.364 AC: 15113 AN: 41480

American (AMR) AF: 0.337 AC: 5149 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3468

East Asian (EAS) AF: 0.150 AC: 778 AN: 5184

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4816

European-Finnish (FIN) AF: 0.277 AC: 2930 AN: 10590

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28818 AN: 67948

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.410 Hom.: 23645

Bravo AF: 0.377

Asia WGS AF: 0.219 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9524596; hg19: chr13-95368839;