rs1992695

chr4-136890593-A-Gchr4-136890593-A-T

Variant summary

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

The NR_149105.1(LINC02511):n.155+25582T>C 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 0.491 in 151,956 control chromosomes in the GnomAD database, including 18,573 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 0.49 (18573 hom., cov: 32)
• Consequence: LINC02511 NR_149105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02511	NR_149105.1	n.155+25582T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02511	ENST00000656956.1	n.129+25582T>C		intron_variant, non_coding_transcript_variant
LINC02511	ENST00000505736.5	n.155+25582T>C		intron_variant, non_coding_transcript_variant		5
LINC02511	ENST00000512039.1	n.93+25582T>C		intron_variant, non_coding_transcript_variant		3
LINC02511	ENST00000652184.1	n.240-76862T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74479 AN: 151838 Hom.: 18559 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.491 AC: 74539 AN: 151956 Hom.: 18573 Cov.: 32 AF XY: 0.491 AC XY: 36450 AN XY: 74238

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.495

Alfa AF: 0.452 Hom.: 9253

Bravo AF: 0.498

Asia WGS AF: 0.478 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.56
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992695; hg19: chr4-137811747;