rs17119490

Variant names:

• chr10-105763169-G-A
• rs17119490
• ENST00000836854.1:n.448+54749C>T

Variant summary

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

The ENST00000836854.1(LINC02627):​n.448+54749C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,100 control chromosomes in the GnomAD database, including 667 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 0.061 (667 hom., cov: 32)
• Consequence: LINC02627 ENST00000836854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02627	NR_120625.1	n.430+54749C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02627	ENST00000836854.1	n.448+54749C>T		intron_variant	Intron 3 of 7
LINC02627	ENST00000836855.1	n.394+54749C>T		intron_variant	Intron 3 of 5
LINC02627	ENST00000836856.1	n.447-42380C>T		intron_variant	Intron 3 of 6
LINC02627	ENST00000836857.1	n.300+54749C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9303 AN: 151982 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.00785

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0613 AC: 9321 AN: 152100 Hom.: 667 Cov.: 32 AF XY: 0.0614 AC XY: 4565 AN XY: 74366

African (AFR) AF: 0.174 AC: 7212 AN: 41488

American (AMR) AF: 0.0251 AC: 384 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.0415 AC: 214 AN: 5158

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4820

European-Finnish (FIN) AF: 0.00785 AC: 83 AN: 10574

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

European-Non Finnish (NFE) AF: 0.0106 AC: 720 AN: 67996

Other (OTH) AF: 0.0655 AC: 138 AN: 2108

Alfa AF: 0.0308 Hom.: 110

Bravo AF: 0.0664

Asia WGS AF: 0.101 AC: 350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.57
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs17119490; hg19: chr10-107522927;