ENST00000415700.2:n.152+2975C>A

Variant names:

• chr2-865143-G-T
• rs4358154
• ENST00000415700.2:n.152+2975C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415700.2(LINC01115):​n.152+2975C>A variant causes a intron 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 ENST00000415700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01115	NR_033880.3	n.309+2975C>A		intron_variant	Intron 1 of 3
LINC01115	NR_111963.1	n.309+2975C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01115	ENST00000415700.2	n.152+2975C>A		intron_variant	Intron 1 of 2	1
LINC01115	ENST00000621134.4	n.309+2975C>A		intron_variant	Intron 1 of 3	1
LINC01115	ENST00000648115.1	n.491+2975C>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.206 AC: 8567 AN: 41526

American (AMR) AF: 0.352 AC: 5382 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1420 AN: 3460

East Asian (EAS) AF: 0.561 AC: 2892 AN: 5158

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4818

European-Finnish (FIN) AF: 0.444 AC: 4694 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27808 AN: 67958

Other (OTH) AF: 0.348 AC: 735 AN: 2110

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
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs4358154; hg19: chr2-860829;