ENST00000814385.1:n.414-8721G>T

Variant names:

• chr2-176869884-G-T
• rs1405613
• ENST00000814385.1:n.414-8721G>T

Variant summary

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

The ENST00000814385.1(LINC01117):​n.414-8721G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,980 control chromosomes in the GnomAD database, including 22,352 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 0.52 (22352 hom., cov: 32)
• Consequence: LINC01117 ENST00000814385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 2 publications found

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01117	ENST00000814385.1	n.414-8721G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79609 AN: 151862 Hom.: 22347 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.524 AC: 79641 AN: 151980 Hom.: 22352 Cov.: 32 AF XY: 0.531 AC XY: 39436 AN XY: 74286

African (AFR) AF: 0.366 AC: 15148 AN: 41434

American (AMR) AF: 0.626 AC: 9558 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4977 AN: 5174

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5720 AN: 10560

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37070 AN: 67946

Other (OTH) AF: 0.534 AC: 1121 AN: 2100

Alfa AF: 0.547 Hom.: 9974

Bravo AF: 0.521

Asia WGS AF: 0.792 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.49
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs1405613; hg19: chr2-177734612;