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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665450.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX21-AS1	ENST00000665450.1		n.132+13000A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9524596;

hg19: chr13-95368839;