5-1359823-T-C

Variant names:

• chr5-1359823-T-C
• rs27064
• ENST00000653645.1:n.437-4288A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653645.1(LINC01511):​n.437-4288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,236 control chromosomes in the GnomAD database, including 53,891 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 0.84 (53891 hom., cov: 34)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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.437-4288A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127794 AN: 152118 Hom.: 53867 Cov.: 34

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.840 AC: 127873 AN: 152236 Hom.: 53891 Cov.: 34 AF XY: 0.838 AC XY: 62365 AN XY: 74420

African (AFR) AF: 0.810 AC: 33649 AN: 41540

American (AMR) AF: 0.821 AC: 12544 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3470

East Asian (EAS) AF: 0.733 AC: 3800 AN: 5182

South Asian (SAS) AF: 0.783 AC: 3779 AN: 4828

European-Finnish (FIN) AF: 0.888 AC: 9407 AN: 10588

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59255 AN: 68020

Other (OTH) AF: 0.833 AC: 1762 AN: 2114

Alfa AF: 0.852 Hom.: 38115

Bravo AF: 0.835

Asia WGS AF: 0.779 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.30
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs27064; hg19: chr5-1359938;