rs1445517

Variant names:

• chr4-136880845-G-C
• rs1445517
• ENST00000505736.5:n.155+35330C>G

Variant summary

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

The ENST00000512039.1(LINC02511):​n.93+35330C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,574 control chromosomes in the GnomAD database, including 17,311 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 0.48 (17311 hom., cov: 31)
• Consequence: LINC02511 ENST00000512039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 3 publications found

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

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 = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512039.1. 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
	LINC02511	NR_149105.1		n.155+35330C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02511	ENST00000505736.5	TSL:5	n.155+35330C>G		intron	N/A
	LINC02511	ENST00000512039.1	TSL:3	n.93+35330C>G		intron	N/A
	LINC02511	ENST00000652184.1		n.240-67114C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72102 AN: 151456 Hom.: 17303 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.476 AC: 72146 AN: 151574 Hom.: 17311 Cov.: 31 AF XY: 0.477 AC XY: 35286 AN XY: 74004

African (AFR) AF: 0.526 AC: 21774 AN: 41384

American (AMR) AF: 0.486 AC: 7387 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2804 AN: 5102

South Asian (SAS) AF: 0.402 AC: 1938 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5090 AN: 10504

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30320 AN: 67784

Other (OTH) AF: 0.482 AC: 1015 AN: 2104

Alfa AF: 0.454 Hom.: 1974

Bravo AF: 0.482

Asia WGS AF: 0.467 AC: 1626 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	13
DANN	Benign	0.73
PhyloP100		0.68

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: rs1445517;

hg19: chr4-137801999;