rs62329728

Variant names:

• chr5-1356775-G-A
• rs62329728
• ENST00000653645.1:n.437-1240C>T

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-1240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 152,272 control chromosomes in the GnomAD database, including 213 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 0.048 (213 hom., cov: 33)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0608 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.437-1240C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7273 AN: 152154 Hom.: 213 Cov.: 33

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.0785

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0478 AC: 7278 AN: 152272 Hom.: 213 Cov.: 33 AF XY: 0.0473 AC XY: 3523 AN XY: 74454

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.0785

Gnomad4 NFE AF: 0.0624

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0567 Hom.: 28

Bravo AF: 0.0433

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62329728; hg19: chr5-1356890;