rs6889886

Positions:

• chr5-1358707-C-T

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-3172G>A 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 0.235 in 152,158 control chromosomes in the GnomAD database, including 4,405 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 0.23 (4405 hom., cov: 33)
• Consequence: LINC01511 ENST00000653645.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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.437-3172G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35707 AN: 152040 Hom.: 4399 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.235 AC: 35709 AN: 152158 Hom.: 4405 Cov.: 33 AF XY: 0.231 AC XY: 17204 AN XY: 74386

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.257

Alfa AF: 0.249 Hom.: 719

Bravo AF: 0.230

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6889886; hg19: chr5-1358822;