6-84468550-T-C

Variant names:

• chr6-84468550-T-C
• rs9362054
• ENST00000428896.1:n.217+2241A>G

Variant summary

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

The ENST00000454172.6(LINC01611):​n.554-24099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,840 control chromosomes in the GnomAD database, including 20,588 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 0.52 (20588 hom., cov: 31)
• Consequence: LINC01611 ENST00000454172.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 16 publications found

Genes affected

LINC01611 (HGNC:51791): (long intergenic non-protein coding RNA 1611)

ENSG00000303044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454172.6. 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
	LINC01611	NR_132100.1		n.217+2241A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01611	ENST00000428896.1	TSL:5	n.217+2241A>G		intron	N/A
	LINC01611	ENST00000454172.6	TSL:3	n.554-24099A>G		intron	N/A
	LINC01611	ENST00000454981.6	TSL:3	n.330+2241A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78672 AN: 151722 Hom.: 20555 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.519 AC: 78763 AN: 151840 Hom.: 20588 Cov.: 31 AF XY: 0.519 AC XY: 38522 AN XY: 74172

African (AFR) AF: 0.461 AC: 19081 AN: 41392

American (AMR) AF: 0.525 AC: 8006 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3545 AN: 5142

South Asian (SAS) AF: 0.530 AC: 2550 AN: 4814

European-Finnish (FIN) AF: 0.511 AC: 5392 AN: 10552

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36149 AN: 67912

Other (OTH) AF: 0.553 AC: 1164 AN: 2106

Alfa AF: 0.536 Hom.: 97107

Bravo AF: 0.520

Asia WGS AF: 0.623 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-0.44

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: rs9362054;

hg19: chr6-85178268;