rs7633815

Variant names:

• chr3-181738126-A-C
• rs7633815
• ENST00000466034.7:n.518-1443A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-181738126-A-C
• chr3-181738126-A-G

Variant summary

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

The ENST00000466034.7(SOX2-OT):​n.518-1443A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,032 control chromosomes in the GnomAD database, including 33,612 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 0.66 (33612 hom., cov: 31)
• Consequence: SOX2-OT ENST00000466034.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

Genes affected

SOX2-OT (HGNC:20209): (SOX2 overlapping transcript) This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX2-OT	NR_004053.3	n.876-1443A>C		intron_variant	Intron 4 of 4
SOX2-OT	NR_075089.1	n.768-1443A>C		intron_variant	Intron 3 of 3
SOX2-OT	NR_075090.1	n.482-1443A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000466034.7	n.518-1443A>C		intron_variant	Intron 2 of 2	1
SOX2-OT	ENST00000476964.6	n.482-1443A>C		intron_variant	Intron 2 of 2	1
SOX2-OT	ENST00000491282.6	n.594-1443A>C		intron_variant	Intron 4 of 4	1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100347 AN: 151914 Hom.: 33564 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.661 AC: 100443 AN: 152032 Hom.: 33612 Cov.: 31 AF XY: 0.658 AC XY: 48908 AN XY: 74306

African (AFR) AF: 0.759 AC: 31447 AN: 41454

American (AMR) AF: 0.735 AC: 11231 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2100 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3321 AN: 5164

South Asian (SAS) AF: 0.535 AC: 2581 AN: 4820

European-Finnish (FIN) AF: 0.601 AC: 6344 AN: 10552

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41277 AN: 67996

Other (OTH) AF: 0.655 AC: 1374 AN: 2098

Alfa AF: 0.635 Hom.: 37520

Bravo AF: 0.680

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7633815; hg19: chr3-181455914;