chr10-26680688-A-G

Variant names:

• chr10-26680688-A-G
• rs1780177
• ENST00000446557.2:n.329+250T>C

Variant summary

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

The ENST00000446557.2(ENSG00000293509):​n.329+250T>C variant causes a intron 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: ENSG00000293509 ENST00000446557.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

ENSG00000293509 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293509	ENST00000446557.2	n.329+250T>C		intron_variant	Intron 3 of 5	2
SELENOOLP	ENST00000636744.2	n.845+250T>C		intron_variant	Intron 6 of 9	6
ENSG00000293509	ENST00000751748.1	n.117+953T>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.570 AC: 23593 AN: 41412

American (AMR) AF: 0.642 AC: 9800 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2467 AN: 3466

East Asian (EAS) AF: 0.892 AC: 4614 AN: 5170

South Asian (SAS) AF: 0.792 AC: 3813 AN: 4814

European-Finnish (FIN) AF: 0.637 AC: 6725 AN: 10554

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47690 AN: 68000

Other (OTH) AF: 0.702 AC: 1483 AN: 2114

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1780177; hg19: chr10-26969617;