rs4085649

chr1-83159053-G-T

Variant summary

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

The NR_147074.1(LINC01362):n.1540-1553G>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 0.237 in 151,370 control chromosomes in the GnomAD database, including 4,911 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 0.24 (4911 hom., cov: 29)
• Consequence: LINC01362 NR_147074.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.69

Genes affected

LINC01362 (HGNC:50596): (long intergenic non-protein coding RNA 1362)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01362	NR_147074.1	n.1540-1553G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01362	ENST00000452901.5	n.1540-1553G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35828 AN: 151250 Hom.: 4911 Cov.: 29

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.237 AC: 35819 AN: 151370 Hom.: 4911 Cov.: 29 AF XY: 0.234 AC XY: 17277 AN XY: 73924

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.255

Alfa AF: 0.248 Hom.: 632

Bravo AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.040
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4085649; hg19: chr1-83624736;