ENST00000415700.2:n.152+17657G>A

Variant names:

• chr2-850461-C-T
• rs4533500
• ENST00000415700.2:n.152+17657G>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+17657G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,052 control chromosomes in the GnomAD database, including 30,415 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 0.62 (30415 hom., cov: 33)
• Consequence: LINC01115 ENST00000415700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415700.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01115	NR_033880.3		n.546+3518G>A		intron	N/A
	LINC01115	NR_111963.1		n.309+17657G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01115	ENST00000415700.2	TSL:1	n.152+17657G>A		intron	N/A
	LINC01115	ENST00000621134.4	TSL:1	n.546+3518G>A		intron	N/A
	LINC01115	ENST00000648115.1		n.491+17657G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94877 AN: 151934 Hom.: 30362 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.625 AC: 94982 AN: 152052 Hom.: 30415 Cov.: 33 AF XY: 0.620 AC XY: 46091 AN XY: 74332

African (AFR) AF: 0.792 AC: 32877 AN: 41498

American (AMR) AF: 0.565 AC: 8625 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2053 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3084 AN: 5150

South Asian (SAS) AF: 0.409 AC: 1972 AN: 4818

European-Finnish (FIN) AF: 0.606 AC: 6410 AN: 10570

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37959 AN: 67954

Other (OTH) AF: 0.609 AC: 1284 AN: 2108

Alfa AF: 0.579 Hom.: 32594

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4533500; hg19: chr2-846164;