10-61067194-C-T

Variant names:

• chr10-61067194-C-T
• rs7922793
• ENST00000687498.2:n.176+65976C>T

Variant summary

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

The ENST00000687498.2(LINC00845):​n.176+65976C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,034 control chromosomes in the GnomAD database, including 37,134 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 0.69 (37134 hom., cov: 31)
• Consequence: LINC00845 ENST00000687498.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 8 publications found

Genes affected

LINC00845 (HGNC:45033): (long intergenic non-protein coding RNA 845)

ENSG00000298595 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687498.2. 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
	LINC00845	ENST00000687498.2		n.176+65976C>T		intron	N/A
	LINC00845	ENST00000756399.1		n.177-8524C>T		intron	N/A
	ENSG00000298595	ENST00000756724.1		n.154+1135G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104629 AN: 151914 Hom.: 37100 Cov.: 31

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.689 AC: 104718 AN: 152034 Hom.: 37134 Cov.: 31 AF XY: 0.683 AC XY: 50728 AN XY: 74312

African (AFR) AF: 0.845 AC: 35088 AN: 41520

American (AMR) AF: 0.660 AC: 10071 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3464

East Asian (EAS) AF: 0.738 AC: 3810 AN: 5164

South Asian (SAS) AF: 0.707 AC: 3413 AN: 4826

European-Finnish (FIN) AF: 0.472 AC: 4973 AN: 10534

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42943 AN: 67948

Other (OTH) AF: 0.681 AC: 1437 AN: 2110

Alfa AF: 0.658 Hom.: 64038

Bravo AF: 0.710

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.79
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs7922793; hg19: chr10-62826952;