rs12659144

Positions:

• chr5-174350517-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125806.1(LINC01411):​n.223+13941T>C variant causes a intron, non coding transcript 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 NR_125806.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01411	NR_125806.1	n.223+13941T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01411	ENST00000507361.5	n.223+13941T>C		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000510234.5	n.82+13941T>C		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000515513.5	n.282+13941T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.177

Alfa AF: 0.154 Hom.: 3955

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12659144; hg19: chr5-173777520;