NR_145452.1:n.4604G>A

Variant names:

• chr18-55776198-C-T
• rs931040
• NR_145452.1:n.4604G>A

Variant summary

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

The NR_145452.1(LINC01415):​n.4604G>A 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 0.887 in 152,208 control chromosomes in the GnomAD database, including 60,216 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 0.89 (60216 hom., cov: 31)
• Consequence: LINC01415 NR_145452.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 4 publications found

Genes affected

LINC01415 (HGNC:50709): (long intergenic non-protein coding RNA 1415)

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_145452.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01415	NR_145452.1		n.4604G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC01415	NR_145453.1		n.4106G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC01415	NR_145454.1		n.3896G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267284	ENST00000587346.1	TSL:4	n.519+3427C>T		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.218-8701C>T		intron	N/A
	ENSG00000267284	ENST00000654829.1		n.157-8701C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134963 AN: 152090 Hom.: 60154 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.887 AC: 135081 AN: 152208 Hom.: 60216 Cov.: 31 AF XY: 0.889 AC XY: 66120 AN XY: 74406

African (AFR) AF: 0.970 AC: 40282 AN: 41526

American (AMR) AF: 0.923 AC: 14119 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5182

South Asian (SAS) AF: 0.786 AC: 3782 AN: 4814

European-Finnish (FIN) AF: 0.872 AC: 9233 AN: 10588

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56841 AN: 68016

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.847 Hom.: 2911

Bravo AF: 0.900

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.64
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs931040; hg19: chr18-53443429;