rs1107748

chr17-43696446-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.289-8983T>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 0.53 in 151,970 control chromosomes in the GnomAD database, including 23,904 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 (23904 hom., cov: 31)
• Consequence: LINC02594 NR_184089.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02594	NR_184089.1	n.289-8983T>C		intron_variant, non_coding_transcript_variant
LINC02594	NR_184090.1	n.475-8983T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02594	ENST00000593169.2	n.196-8983T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80410 AN: 151852 Hom.: 23863 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.530 AC: 80498 AN: 151970 Hom.: 23904 Cov.: 31 AF XY: 0.529 AC XY: 39270 AN XY: 74282

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.474

Alfa AF: 0.422 Hom.: 19757

Bravo AF: 0.544

Asia WGS AF: 0.374 AC: 1303 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	7.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107748; hg19: chr17-41773814;