rs188655146

Variant names:

• chr3-86495236-T-G
• rs188655146
• ENST00000460586.1:n.116-555T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000460586.1(LINC02070):​n.116-555T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0050 (4 hom., cov: 19)
• Consequence: LINC02070 ENST00000460586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 1 publications found

Genes affected

LINC02070 (HGNC:52916): (long intergenic non-protein coding RNA 2070)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00496 (329/66302) while in subpopulation AFR AF = 0.0292 (257/8816). AF 95% confidence interval is 0.0262. There are 4 homozygotes in GnomAd4. There are 166 alleles in the male GnomAd4 subpopulation. Median coverage is 19. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460586.1. 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
	LINC02070	NR_135563.1		n.116-555T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02070	ENST00000460586.1	TSL:1	n.116-555T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00495 AC: 328 AN: 66300 Hom.: 4 Cov.: 19

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00267

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00143

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0321

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.00572

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

GnomAD4 genome AF: 0.00496 AC: 329 AN: 66302 Hom.: 4 Cov.: 19 AF XY: 0.00538 AC XY: 166 AN XY: 30838

African (AFR) AF: 0.0292 AC: 257 AN: 8816

American (AMR) AF: 0.00266 AC: 17 AN: 6390

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2060

East Asian (EAS) AF: 0.00 AC: 0 AN: 2492

South Asian (SAS) AF: 0.00144 AC: 3 AN: 2080

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2894

Middle Eastern (MID) AF: 0.0352 AC: 5 AN: 142

European-Non Finnish (NFE) AF: 0.00105 AC: 42 AN: 39870

Other (OTH) AF: 0.00567 AC: 5 AN: 882

Alfa AF: 0.0185 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.36
PhyloP100		0.029

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: rs188655146;

hg19: chr3-86544386;