5-1356829-C-T

Position:

• chr5-1356829-C-T

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-1294G>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 0.493 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01511	ENST00000653645.1	n.437-1294G>A		intron_variant, non_coding_transcript_variant

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;