rs1780177

chr10-26680688-A-G

Variant summary

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

The ENST00000636744.1(SELENOOLP):n.845+250T>C 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 0.664 in 152,012 control chromosomes in the GnomAD database, including 33,940 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 (33940 hom., cov: 31)
• Consequence: SELENOOLP ENST00000636744.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

SELENOOLP (HGNC:53787): (selenoprotein O like, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELENOOLP	ENST00000636744.1	n.845+250T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100853 AN: 151894 Hom.: 33924 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.664 AC: 100906 AN: 152012 Hom.: 33940 Cov.: 31 AF XY: 0.662 AC XY: 49154 AN XY: 74306

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.702

Alfa AF: 0.676 Hom.: 4365

Bravo AF: 0.658

Asia WGS AF: 0.827 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.61
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780177; hg19: chr10-26969617;