5-174469021-G-C

Variant names:

• chr5-174469021-G-C
• rs1087518
• ENST00000507361.5:n.335+41271G>C

Variant summary

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

The ENST00000507361.5(LINC01411):​n.335+41271G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,512 control chromosomes in the GnomAD database, including 37,622 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 0.70 (37622 hom., cov: 31)
• Consequence: LINC01411 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 0 publications found

Genes affected

LINC01411 (HGNC:50703): (long intergenic non-protein coding RNA 1411)

ENSG00000298768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507361.5. 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
	LINC01411	NR_125806.1		n.335+41271G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01411	ENST00000507361.5	TSL:3	n.335+41271G>C		intron	N/A
	LINC01411	ENST00000510234.6	TSL:3	n.297+41271G>C		intron	N/A
	LINC01411	ENST00000515513.5	TSL:5	n.394+41271G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105724 AN: 151394 Hom.: 37606 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.698 AC: 105772 AN: 151512 Hom.: 37622 Cov.: 31 AF XY: 0.706 AC XY: 52261 AN XY: 74064

African (AFR) AF: 0.569 AC: 23474 AN: 41244

American (AMR) AF: 0.788 AC: 12017 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2221 AN: 3462

East Asian (EAS) AF: 0.998 AC: 5150 AN: 5158

South Asian (SAS) AF: 0.867 AC: 4179 AN: 4820

European-Finnish (FIN) AF: 0.720 AC: 7567 AN: 10504

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 48913 AN: 67770

Other (OTH) AF: 0.710 AC: 1500 AN: 2114

Alfa AF: 0.711 Hom.: 4833

Bravo AF: 0.696

Asia WGS AF: 0.917 AC: 3177 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.16
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1087518;

hg19: chr5-173896024;