rs3094315

Variant names:

• chr1-817186-G-A
• rs3094315
• ENST00000744085.1:n.1093C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-817186-G-A
• chr1-817186-G-T

Variant summary

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

The ENST00000744085.1(LINC00115):​n.1093C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,044 control chromosomes in the GnomAD database, including 40,155 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 0.71 (40155 hom., cov: 33)
• Consequence: LINC00115 ENST00000744085.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 22 publications found

Genes affected

LINC00115 (HGNC:26211): (long intergenic non-protein coding RNA 115)

FAM87B (HGNC:32236): (family with sequence similarity 87 member B)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM87B	NR_103536.1	n.-185G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00115	ENST00000744085.1	n.1093C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00115	ENST00000744086.1	n.1094C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00115	ENST00000447500.5	n.1030+187C>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108166 AN: 151926 Hom.: 40145 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.712 AC: 108218 AN: 152044 Hom.: 40155 Cov.: 33 AF XY: 0.713 AC XY: 53015 AN XY: 74338

African (AFR) AF: 0.436 AC: 18065 AN: 41442

American (AMR) AF: 0.785 AC: 11994 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2711 AN: 3456

East Asian (EAS) AF: 0.888 AC: 4611 AN: 5192

South Asian (SAS) AF: 0.791 AC: 3814 AN: 4820

European-Finnish (FIN) AF: 0.797 AC: 8429 AN: 10578

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56118 AN: 67958

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.800 Hom.: 82146

Asia WGS AF: 0.807 AC: 2807 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	2.4
DANN	Benign	0.71
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs3094315; hg19: chr1-752566;