rs1031912

Positions:

• chr15-94046999-T-C

Variant summary

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

The NR_120320.1(LINC01581):​n.1141+35276A>G 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 0.0421 in 152,300 control chromosomes in the GnomAD database, including 181 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 0.042 (181 hom., cov: 33)
• Consequence: LINC01581 NR_120320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

LINC01581 (HGNC:51415): (long intergenic non-protein coding RNA 1581)

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.1141+35276A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.1141+35276A>G		intron_variant, non_coding_transcript_variant		1
LINC01579	ENST00000556447.5	n.409-16598A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6404 AN: 152182 Hom.: 180 Cov.: 33

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.00753

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0421 AC: 6415 AN: 152300 Hom.: 181 Cov.: 33 AF XY: 0.0424 AC XY: 3161 AN XY: 74476

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.00753

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0393 Hom.: 188

Bravo AF: 0.0437

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
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: rs1031912; hg19: chr15-94590228;