rs16910421

Positions:

• chr11-12049118-G-A

Variant summary

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

The NR_135109.1(LINC02547):​n.57-9416G>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 0.0442 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 NR_135109.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02547	NR_135109.1	n.57-9416G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02547	ENST00000531559.1	n.57-9416G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.00695

Gnomad4 SAS AF: 0.0540

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0330 Hom.: 95

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16910421; hg19: chr11-12070665;