17-43677088-C-T

Variant summary

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

The NR_184089.1(LINC02594):n.189-3178C>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 0.525 in 152,170 control chromosomes in the GnomAD database, including 22,603 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 0.53 (22603 hom., cov: 33)
• Consequence: LINC02594 NR_184089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

LINC02594 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02594	NR_184089.1	n.189-3178C>T		intron_variant, non_coding_transcript_variant
LOC107985085	XR_001752895.2	n.199-23G>A		intron_variant, non_coding_transcript_variant
LOC107985085	XR_001752894.2	n.89-23G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79876 AN: 152052 Hom.: 22563 Cov.: 33

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.525 AC: 79958 AN: 152170 Hom.: 22603 Cov.: 33 AF XY: 0.528 AC XY: 39286 AN XY: 74382

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.488

Alfa AF: 0.491 Hom.: 3083

Bravo AF: 0.533

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8070993; hg19: chr17-41754456; COSMIC: COSV74166957;