rs1465531

Positions:

• chr2-144522585-A-G
• chr2-144522585-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110570.1(LINC01412):​n.59+659A>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 0.87 in 151,046 control chromosomes in the GnomAD database, including 59,667 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 0.87 (59667 hom., cov: 26)
• Consequence: LINC01412 NR_110570.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99

Genes affected

LINC01412 (HGNC:50704): (long intergenic non-protein coding RNA 1412)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01412	NR_110570.1	n.59+659A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01412	ENST00000696348.1	n.59+659A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.870 AC: 131386 AN: 150936 Hom.: 59638 Cov.: 26

Gnomad AFR AF: 0.578

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.870 AC: 131459 AN: 151046 Hom.: 59667 Cov.: 26 AF XY: 0.875 AC XY: 64508 AN XY: 73762

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.895

Alfa AF: 0.942 Hom.: 13383

Bravo AF: 0.852

Asia WGS AF: 0.945 AC: 3285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	15
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1465531; hg19: chr2-145280152;