rs4380275

Variant names:

• chr2-773278-C-T
• rs4380275
• ENST00000783116.1:n.417+32751G>A

Variant summary

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

The ENST00000783116.1(LINC01115):​n.417+32751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,118 control chromosomes in the GnomAD database, including 39,940 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 0.72 (39940 hom., cov: 33)
• Consequence: LINC01115 ENST00000783116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 9 publications found

Genes affected

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

ENSG00000223751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373480	XR_007086095.1	n.2151-3558C>T		intron_variant	Intron 2 of 3
LOC105373480	XR_007086101.1	n.2368-3558C>T		intron_variant	Intron 3 of 6
LOC105373480	XR_007086107.1	n.1715-3558C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01115	ENST00000783116.1	n.417+32751G>A		intron_variant	Intron 2 of 2
LINC01115	ENST00000783117.1	n.501-31225G>A		intron_variant	Intron 2 of 2
LINC01115	ENST00000783118.1	n.419-19836G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109213 AN: 151998 Hom.: 39881 Cov.: 33

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.719 AC: 109335 AN: 152118 Hom.: 39940 Cov.: 33 AF XY: 0.720 AC XY: 53512 AN XY: 74350

African (AFR) AF: 0.860 AC: 35699 AN: 41530

American (AMR) AF: 0.737 AC: 11258 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.737 AC: 3807 AN: 5164

South Asian (SAS) AF: 0.800 AC: 3861 AN: 4826

European-Finnish (FIN) AF: 0.638 AC: 6735 AN: 10558

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43707 AN: 67978

Other (OTH) AF: 0.699 AC: 1476 AN: 2112

Alfa AF: 0.664 Hom.: 148709

Bravo AF: 0.728

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.37
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4380275; hg19: chr2-773278;