rs188655146

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02070	NR_135563.1	n.116-555T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02070	ENST00000460586.1	n.116-555T>G		intron_variant	Intron 1 of 1	1

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

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.00266

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00144

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00105

Gnomad4 OTH AF: 0.00567

Alfa AF: 0.0185 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs188655146; hg19: chr3-86544386;