rs1718031

chr2-108175186-G-A

Variant summary

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

The NR_131251.1(LINC01594):n.500+3968C>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 0.323 in 151,936 control chromosomes in the GnomAD database, including 8,239 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 0.32 (8239 hom., cov: 31)
• Consequence: LINC01594 NR_131251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

LINC01594 (HGNC:51584): (long intergenic non-protein coding RNA 1594)

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 (SAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01594	NR_131251.1	n.500+3968C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01594	ENST00000445083.2	n.545+3968C>T		intron_variant, non_coding_transcript_variant		5
LINC01594	ENST00000666270.1	n.382+3968C>T		intron_variant, non_coding_transcript_variant
LINC01594	ENST00000669479.1	n.424+3968C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49019 AN: 151818 Hom.: 8226 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.323 AC: 49083 AN: 151936 Hom.: 8239 Cov.: 31 AF XY: 0.324 AC XY: 24080 AN XY: 74244

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.0919

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.320

Alfa AF: 0.346 Hom.: 15181

Bravo AF: 0.309

Asia WGS AF: 0.307 AC: 1065 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	3.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1718031; hg19: chr2-108791642;