ENST00000693438.3:n.883G>A

Variant names:

• chr10-100372886-C-T
• rs570844
• ENST00000693438.3:n.883G>A

Variant summary

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

The ENST00000693438.3(ENSG00000289301):​n.883G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,280 control chromosomes in the GnomAD database, including 231 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 0.039 (231 hom., cov: 31)
• Consequence: ENSG00000289301 ENST00000693438.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 4 publications found

Genes affected

ENSG00000289301 (HGNC:):

OLMALINC (HGNC:28060): (oligodendrocyte maturation-associated long intergenic non-coding RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 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
ENSG00000289301	ENST00000693438.3	n.883G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289301	ENST00000769404.1	n.343+114G>A		intron_variant	Intron 1 of 1
ENSG00000289301	ENST00000769405.1	n.395+114G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5913 AN: 152162 Hom.: 232 Cov.: 31

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00645

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0389 AC: 5928 AN: 152280 Hom.: 231 Cov.: 31 AF XY: 0.0424 AC XY: 3159 AN XY: 74464

African (AFR) AF: 0.0823 AC: 3416 AN: 41528

American (AMR) AF: 0.0249 AC: 381 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3472

East Asian (EAS) AF: 0.112 AC: 582 AN: 5194

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4828

European-Finnish (FIN) AF: 0.0635 AC: 674 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00645 AC: 439 AN: 68032

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0178 Hom.: 85

Bravo AF: 0.0366

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs570844; hg19: chr10-102132643;