chr10-105756594-T-C

Variant names:

• chr10-105756594-T-C
• rs17119461
• ENST00000836854.1:n.448+61324A>G

Variant summary

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

The ENST00000836854.1(LINC02627):​n.448+61324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,282 control chromosomes in the GnomAD database, including 1,075 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 0.075 (1075 hom., cov: 33)
• Consequence: LINC02627 ENST00000836854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 23 publications found

Genes affected

LINC02627 (HGNC:54106): (long intergenic non-protein coding RNA 2627)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836854.1. 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
	LINC02627	NR_120625.1		n.430+61324A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02627	ENST00000836854.1		n.448+61324A>G		intron	N/A
	LINC02627	ENST00000836855.1		n.394+61324A>G		intron	N/A
	LINC02627	ENST00000836856.1		n.447-35805A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11349 AN: 152164 Hom.: 1074 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.00791

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0747 AC: 11372 AN: 152282 Hom.: 1075 Cov.: 33 AF XY: 0.0744 AC XY: 5541 AN XY: 74462

African (AFR) AF: 0.222 AC: 9199 AN: 41520

American (AMR) AF: 0.0288 AC: 441 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3470

East Asian (EAS) AF: 0.0412 AC: 214 AN: 5194

South Asian (SAS) AF: 0.0826 AC: 399 AN: 4830

European-Finnish (FIN) AF: 0.00791 AC: 84 AN: 10626

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0106 AC: 724 AN: 68030

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0283 Hom.: 997

Bravo AF: 0.0824

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.59
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs17119461; hg19: chr10-107516352;