rs12659144

Variant names:

• chr5-174350517-T-C
• rs12659144
• ENST00000507361.5:n.223+13941T>C

Variant summary

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

The ENST00000507361.5(LINC01411):​n.223+13941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,008 control chromosomes in the GnomAD database, including 2,749 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 0.18 (2749 hom., cov: 32)
• Consequence: LINC01411 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01411	NR_125806.1	n.223+13941T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000507361.5	n.223+13941T>C		intron_variant	Intron 1 of 3	3
LINC01411	ENST00000510234.6	n.185+13941T>C		intron_variant	Intron 2 of 6	3
LINC01411	ENST00000515513.5	n.282+13941T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27336 AN: 151894 Hom.: 2733 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.180 AC: 27385 AN: 152008 Hom.: 2749 Cov.: 32 AF XY: 0.180 AC XY: 13398 AN XY: 74304

African (AFR) AF: 0.253 AC: 10469 AN: 41426

American (AMR) AF: 0.111 AC: 1692 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1744 AN: 5150

South Asian (SAS) AF: 0.151 AC: 728 AN: 4812

European-Finnish (FIN) AF: 0.154 AC: 1624 AN: 10578

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9946 AN: 67972

Other (OTH) AF: 0.177 AC: 372 AN: 2104

Alfa AF: 0.158 Hom.: 8879

Bravo AF: 0.183

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs12659144; hg19: chr5-173777520;