chr5-174339427-G-A

Variant names:

• chr5-174339427-G-A
• rs17077348
• ENST00000507361.5:n.223+2851G>A

Variant summary

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

The ENST00000507361.5(LINC01411):​n.223+2851G>A variant causes a intron 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 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.083 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.223+2851G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01411	ENST00000507361.5	TSL:3	n.223+2851G>A		intron	N/A
	LINC01411	ENST00000510234.6	TSL:3	n.185+2851G>A		intron	N/A
	LINC01411	ENST00000515513.5	TSL:5	n.282+2851G>A		intron	N/A

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

African (AFR) AF: 0.0853 AC: 3541 AN: 41488

American (AMR) AF: 0.0255 AC: 390 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0665 AC: 231 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4818

European-Finnish (FIN) AF: 0.0235 AC: 249 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0315 AC: 2139 AN: 67984

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0318 Hom.: 136

Bravo AF: 0.0481

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.043
DANN	Benign	0.51
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17077348; hg19: chr5-173766430;