rs9902563

chr17-43679613-T-C

Variant summary

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

The NR_184089.1(LINC02594):n.189-653T>C 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 0.536 in 151,248 control chromosomes in the GnomAD database, including 23,045 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 0.54 (23045 hom., cov: 28)
• Consequence: LINC02594 NR_184089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

Genes affected

LINC02594 (HGNC:53935): (long intergenic non-protein coding RNA 2594)

LOC107985085 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02594	NR_184089.1	n.189-653T>C		intron_variant, non_coding_transcript_variant
LOC107985085	XR_001752895.2	n.199-2548A>G		intron_variant, non_coding_transcript_variant
LINC02594	NR_184090.1	n.374+178T>C		intron_variant, non_coding_transcript_variant
LOC107985085	XR_001752894.2	n.88+1392A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02594	ENST00000593169.2	n.95+178T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81050 AN: 151132 Hom.: 23019 Cov.: 28

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.536 AC: 81116 AN: 151248 Hom.: 23045 Cov.: 28 AF XY: 0.538 AC XY: 39720 AN XY: 73812

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.510

Alfa AF: 0.457 Hom.: 8781

Bravo AF: 0.543

Asia WGS AF: 0.470 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9902563; hg19: chr17-41756981;