rs27065

chr5-1359140-G-Achr5-1359140-G-C

Variant summary

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

The ENST00000653645.1(LINC01511):n.437-3605C>T 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 0.469 in 151,924 control chromosomes in the GnomAD database, including 17,099 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 0.47 (17099 hom., cov: 32)
• Consequence: LINC01511 ENST00000653645.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877

Genes affected

LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01511	ENST00000653645.1	n.437-3605C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71273 AN: 151806 Hom.: 17089 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.469 AC: 71320 AN: 151924 Hom.: 17099 Cov.: 32 AF XY: 0.471 AC XY: 34930 AN XY: 74236

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.455

Alfa AF: 0.491 Hom.: 2352

Bravo AF: 0.468

Asia WGS AF: 0.540 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27065; hg19: chr5-1359255;