10-100372904-C-G

Variant names:

• chr10-100372904-C-G
• rs608622
• ENST00000693438.3:n.865G>C

Variant summary

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

The ENST00000693438.3(ENSG00000289301):​n.865G>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 ENST00000693438.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 2 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693438.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289301	ENST00000693438.3		n.865G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289301	ENST00000769404.1		n.343+96G>C		intron	N/A
	ENSG00000289301	ENST00000769405.1		n.395+96G>C		intron	N/A

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

African (AFR) AF: 0.130 AC: 5395 AN: 41522

American (AMR) AF: 0.0339 AC: 519 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.111 AC: 578 AN: 5184

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4822

European-Finnish (FIN) AF: 0.0635 AC: 673 AN: 10604

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00661 AC: 450 AN: 68028

Other (OTH) AF: 0.0416 AC: 88 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs608622; hg19: chr10-102132661;