rs7659755

Variant names:

• chr4-181087979-G-A
• rs7659755
• ENST00000512487.2:n.526-23499C>T

Variant summary

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

The ENST00000512487.2(LINC00290):​n.526-23499C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,092 control chromosomes in the GnomAD database, including 48,391 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 0.79 (48391 hom., cov: 32)
• Consequence: LINC00290 ENST00000512487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 7 publications found

Genes affected

LINC00290 (HGNC:38515): (long intergenic non-protein coding RNA 290)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512487.2. 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
	LINC00290	NR_033918.1		n.202-23499C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00290	ENST00000512487.2	TSL:1	n.526-23499C>T		intron	N/A
	LINC00290	ENST00000778348.1		n.288-23499C>T		intron	N/A
	LINC00290	ENST00000778349.1		n.236-23499C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120828 AN: 151974 Hom.: 48370 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.795 AC: 120900 AN: 152092 Hom.: 48391 Cov.: 32 AF XY: 0.796 AC XY: 59170 AN XY: 74338

African (AFR) AF: 0.726 AC: 30077 AN: 41452

American (AMR) AF: 0.784 AC: 11979 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5070 AN: 5186

South Asian (SAS) AF: 0.819 AC: 3953 AN: 4824

European-Finnish (FIN) AF: 0.831 AC: 8790 AN: 10572

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.816 AC: 55457 AN: 67998

Other (OTH) AF: 0.816 AC: 1723 AN: 2112

Alfa AF: 0.811 Hom.: 220199

Bravo AF: 0.790

Asia WGS AF: 0.877 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		0.10

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: rs7659755;

hg19: chr4-182009132;