rs17119434

Variant names:

• chr10-105745403-A-G
• rs17119434
• ENST00000836854.1:n.449-71715T>C

Variant summary

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

The ENST00000836854.1(LINC02627):​n.449-71715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,200 control chromosomes in the GnomAD database, including 1,525 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 0.087 (1525 hom., cov: 32)
• Consequence: LINC02627 ENST00000836854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02627	NR_120625.1	n.431-71715T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02627	ENST00000836854.1	n.449-71715T>C		intron_variant	Intron 3 of 7
LINC02627	ENST00000836855.1	n.395-71715T>C		intron_variant	Intron 3 of 5
LINC02627	ENST00000836856.1	n.447-24614T>C		intron_variant	Intron 3 of 6
LINC02627	ENST00000836857.1	n.301-71715T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13246 AN: 152082 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.00772

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0872 AC: 13273 AN: 152200 Hom.: 1525 Cov.: 32 AF XY: 0.0863 AC XY: 6422 AN XY: 74426

African (AFR) AF: 0.264 AC: 10964 AN: 41480

American (AMR) AF: 0.0350 AC: 536 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3470

East Asian (EAS) AF: 0.0422 AC: 218 AN: 5170

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4826

European-Finnish (FIN) AF: 0.00772 AC: 82 AN: 10624

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 740 AN: 68010

Other (OTH) AF: 0.0780 AC: 165 AN: 2116

Alfa AF: 0.0399 Hom.: 355

Bravo AF: 0.0954

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.31
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs17119434; hg19: chr10-107505161;