chr5-1358707-C-T

Variant names:

• chr5-1358707-C-T
• rs6889886
• ENST00000653645.1:n.437-3172G>A

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01511	ENST00000653645.1	n.437-3172G>A		intron_variant	Intron 1 of 1

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;