2-865143-G-T

Position:

• chr2-865143-G-T

Variant summary

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

The NR_111963.1(LINC01115):​n.309+2975C>A 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 0.352 in 152,094 control chromosomes in the GnomAD database, including 9,931 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 0.35 (9931 hom., cov: 33)
• Consequence: LINC01115 NR_111963.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

LINC01115 (HGNC:49258): (long intergenic non-protein coding RNA 1115)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01115	NR_111963.1	n.309+2975C>A		intron_variant, non_coding_transcript_variant
LINC01115	NR_033880.3	n.309+2975C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01115	ENST00000621134.4	n.309+2975C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53462 AN: 151976 Hom.: 9932 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.352 AC: 53482 AN: 152094 Hom.: 9931 Cov.: 33 AF XY: 0.353 AC XY: 26209 AN XY: 74338

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.348

Alfa AF: 0.377 Hom.: 1871

Bravo AF: 0.339

Asia WGS AF: 0.432 AC: 1497 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	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4358154; hg19: chr2-860829;