rs16910421

Variant names:

• chr11-12049118-G-A
• rs16910421
• ENST00000531559.1:n.57-9416G>A

Variant summary

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

The ENST00000531559.1(LINC02547):​n.57-9416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,320 control chromosomes in the GnomAD database, including 230 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 0.044 (230 hom., cov: 33)
• Consequence: LINC02547 ENST00000531559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 5 publications found

Genes affected

LINC02547 (HGNC:53582): (long intergenic non-protein coding RNA 2547)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02547	NR_135109.1	n.57-9416G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02547	ENST00000531559.1	n.57-9416G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6735 AN: 152202 Hom.: 232 Cov.: 33

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0442 AC: 6732 AN: 152320 Hom.: 230 Cov.: 33 AF XY: 0.0432 AC XY: 3220 AN XY: 74472

African (AFR) AF: 0.0887 AC: 3685 AN: 41562

American (AMR) AF: 0.0289 AC: 442 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 232 AN: 3472

East Asian (EAS) AF: 0.00695 AC: 36 AN: 5182

South Asian (SAS) AF: 0.0540 AC: 261 AN: 4830

European-Finnish (FIN) AF: 0.0123 AC: 131 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0267 AC: 1817 AN: 68034

Other (OTH) AF: 0.0455 AC: 96 AN: 2110

Alfa AF: 0.0337 Hom.: 328

Bravo AF: 0.0466

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16910421; hg19: chr11-12070665;