rs62329728

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653645.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01511	ENST00000653645.1		n.437-1240C>T		intron	N/A

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

African (AFR) AF: 0.0233 AC: 969 AN: 41544

American (AMR) AF: 0.0375 AC: 573 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4820

European-Finnish (FIN) AF: 0.0785 AC: 832 AN: 10604

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0624 AC: 4242 AN: 68034

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.52
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs62329728;

hg19: chr5-1356890;