rs1016461

chr6-68326357-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+588T>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 0.453 in 151,896 control chromosomes in the GnomAD database, including 17,454 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 0.45 (17454 hom., cov: 31)
• Consequence: LINC02549 NR_125854.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02549	NR_125854.1	n.237+588T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02549	ENST00000445346.1	n.237+588T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68704 AN: 151778 Hom.: 17428 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.453 AC: 68763 AN: 151896 Hom.: 17454 Cov.: 31 AF XY: 0.457 AC XY: 33916 AN XY: 74240

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.512

Alfa AF: 0.504 Hom.: 9086

Bravo AF: 0.458

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.0
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: rs1016461; hg19: chr6-69036249;