rs12101726

chr15-94038713-A-C

Variant summary

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

The NR_120320.1(LINC01581):n.1142-36954T>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 0.191 in 152,144 control chromosomes in the GnomAD database, including 5,692 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 0.19 (5692 hom., cov: 32)
• Consequence: LINC01581 NR_120320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01581	NR_120320.1	n.1142-36954T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01581	ENST00000558874.1	n.1142-36954T>G		intron_variant, non_coding_transcript_variant		1
LINC01579	ENST00000556447.5	n.409-8312T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28962 AN: 152026 Hom.: 5659 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.191 AC: 29053 AN: 152144 Hom.: 5692 Cov.: 32 AF XY: 0.188 AC XY: 13958 AN XY: 74408

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0755 Hom.: 1436

Bravo AF: 0.215

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.4
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12101726; hg19: chr15-94581942;