rs1445517

chr4-136880845-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_149105.1(LINC02511):n.155+35330C>G variant causes a intron, non coding transcript 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 NR_149105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02511	NR_149105.1	n.155+35330C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02511	ENST00000656956.1	n.129+35330C>G		intron_variant, non_coding_transcript_variant
LINC02511	ENST00000505736.5	n.155+35330C>G		intron_variant, non_coding_transcript_variant		5
LINC02511	ENST00000512039.1	n.93+35330C>G		intron_variant, non_coding_transcript_variant		3
LINC02511	ENST00000652184.1	n.240-67114C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.482

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	13
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1445517; hg19: chr4-137801999;