ENST00000445346.1:n.237+588T>C

Variant names:

• chr6-68326357-A-G
• rs1016461
• ENST00000445346.1:n.237+588T>C

Variant summary

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

The ENST00000445346.1(LINC02549):​n.237+588T>C variant causes a intron 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 ENST00000445346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445346.1. 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
	LINC02549	NR_125854.1		n.237+588T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02549	ENST00000445346.1	TSL:1	n.237+588T>C		intron	N/A

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

African (AFR) AF: 0.232 AC: 9601 AN: 41472

American (AMR) AF: 0.593 AC: 9025 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3472

East Asian (EAS) AF: 0.829 AC: 4251 AN: 5128

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4816

European-Finnish (FIN) AF: 0.464 AC: 4896 AN: 10556

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.508 AC: 34535 AN: 67922

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

Alfa AF: 0.501 Hom.: 10120

Bravo AF: 0.458

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.51
PhyloP100		-0.034

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1016461;

hg19: chr6-69036249;