13-111997186-C-T

Position:

• chr13-111997186-C-T

Variant summary

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

The NR_120392.1(SOX1-OT):​n.84+24793C>T 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 0.485 in 152,082 control chromosomes in the GnomAD database, including 18,302 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 0.49 (18302 hom., cov: 33)
• Consequence: SOX1-OT NR_120392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

SOX1-OT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX1-OT	NR_120392.1	n.84+24793C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73758 AN: 151964 Hom.: 18280 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.485 AC: 73824 AN: 152082 Hom.: 18302 Cov.: 33 AF XY: 0.475 AC XY: 35327 AN XY: 74330

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.465

Alfa AF: 0.506 Hom.: 19364

Bravo AF: 0.493

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0020
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726455; hg19: chr13-112651500;