rs17077348

chr5-174339427-G-Achr5-174339427-G-Cchr5-174339427-G-T

Variant summary

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

The NR_125806.1(LINC01411):n.223+2851G>A 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 0.0446 in 152,134 control chromosomes in the GnomAD database, including 188 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 0.045 (188 hom., cov: 32)
• Consequence: LINC01411 NR_125806.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.083 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01411	NR_125806.1	n.223+2851G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01411	ENST00000507361.5	n.223+2851G>A		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000510234.5	n.82+2851G>A		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000515513.5	n.282+2851G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6777 AN: 152016 Hom.: 188 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0446 AC: 6782 AN: 152134 Hom.: 188 Cov.: 32 AF XY: 0.0433 AC XY: 3223 AN XY: 74382

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.0665

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0235

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0201 Hom.: 14

Bravo AF: 0.0481

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.043
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17077348; hg19: chr5-173766430;