chr5-1356829-C-T

Variant names:

• chr5-1356829-C-T
• rs37002
• ENST00000653645.1:n.437-1294G>A

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-1294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,056 control chromosomes in the GnomAD database, including 19,279 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 (19279 hom., cov: 32)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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.437-1294G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74941 AN: 151938 Hom.: 19259 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.493 AC: 75006 AN: 152056 Hom.: 19279 Cov.: 32 AF XY: 0.483 AC XY: 35918 AN XY: 74322

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.477

Alfa AF: 0.496 Hom.: 2331

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37002; hg19: chr5-1356944;