chr10-61851595-C-A

Variant names:

• chr10-61851595-C-A
• rs2588969
• ENST00000717519.1:n.214+11866G>T

Variant summary

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

The ENST00000717519.1(LINC02625):​n.214+11866G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,634 control chromosomes in the GnomAD database, including 13,351 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 0.41 (13351 hom., cov: 30)
• Consequence: LINC02625 ENST00000717519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 16 publications found

Genes affected

LINC02625 (HGNC:54104): (long intergenic non-protein coding RNA 2625)

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 (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02625	XR_001747458.2	n.184+11866G>T		intron_variant	Intron 2 of 5
LINC02625	XR_001747460.2	n.303+11866G>T		intron_variant	Intron 2 of 5
LINC02625	XR_001747461.2	n.187+11866G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02625	ENST00000717519.1	n.214+11866G>T		intron_variant	Intron 2 of 3
LINC02625	ENST00000717534.1	n.217+11866G>T		intron_variant	Intron 2 of 3
LINC02625	ENST00000717535.1	n.373+11866G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62692 AN: 151512 Hom.: 13334 Cov.: 30

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.414 AC: 62765 AN: 151634 Hom.: 13351 Cov.: 30 AF XY: 0.412 AC XY: 30512 AN XY: 74092

African (AFR) AF: 0.476 AC: 19664 AN: 41282

American (AMR) AF: 0.481 AC: 7336 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1298 AN: 3460

East Asian (EAS) AF: 0.552 AC: 2839 AN: 5142

South Asian (SAS) AF: 0.353 AC: 1695 AN: 4808

European-Finnish (FIN) AF: 0.333 AC: 3501 AN: 10510

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25278 AN: 67884

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.401 Hom.: 3279

Bravo AF: 0.431

Asia WGS AF: 0.499 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2588969; hg19: chr10-63611354;