rs608622

Variant names:

• chr10-100372904-C-G
• rs608622
• ENST00000693438.2:n.490G>C

Variant summary

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

The ENST00000693438.2(ENSG00000289301):​n.490G>C 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 0.053 in 152,258 control chromosomes in the GnomAD database, including 443 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 0.053 (443 hom., cov: 32)
• Consequence: ENSG00000289301 ENST00000693438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

ENSG00000289301 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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	ENST00000693438.2	n.490G>C		non_coding_transcript_exon_variant	Exon 1 of 1
OLMALINC	ENST00000668904.1	n.-195C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8043 AN: 152140 Hom.: 440 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00661

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0530 AC: 8074 AN: 152258 Hom.: 443 Cov.: 32 AF XY: 0.0553 AC XY: 4116 AN XY: 74440

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0635

Gnomad4 NFE AF: 0.00661

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0328 Hom.: 26

Bravo AF: 0.0535

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs608622; hg19: chr10-102132661;