rs2588969

chr10-61851595-C-Achr10-61851595-C-Gchr10-61851595-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747461.2(LINC02625):n.187+11866G>T variant causes a intron, non coding transcript 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 XR_001747461.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

Genes affected

LINC02625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02625	XR_001747461.2	n.187+11866G>T		intron_variant, non_coding_transcript_variant
LINC02625	XR_001747458.2	n.184+11866G>T		intron_variant, non_coding_transcript_variant
LINC02625	XR_001747460.2	n.303+11866G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.417

Alfa AF: 0.402 Hom.: 1544

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2588969; hg19: chr10-63611354;