rs1158811

chr6-68323676-A-G

Variant summary

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

The NR_125854.1(LINC02549):n.237+3269T>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 0.268 in 151,966 control chromosomes in the GnomAD database, including 5,797 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 0.27 (5797 hom., cov: 32)
• Consequence: LINC02549 NR_125854.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

Genes affected

LINC02549 (HGNC:53584): (long intergenic non-protein coding RNA 2549)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02549	NR_125854.1	n.237+3269T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02549	ENST00000445346.1	n.237+3269T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40678 AN: 151848 Hom.: 5786 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.268 AC: 40704 AN: 151966 Hom.: 5797 Cov.: 32 AF XY: 0.267 AC XY: 19834 AN XY: 74278

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0689

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.226

Alfa AF: 0.265 Hom.: 958

Bravo AF: 0.263

Asia WGS AF: 0.159 AC: 551 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1158811; hg19: chr6-69033568;