chr5-1360010-C-G

Variant names:

• chr5-1360010-C-G
• rs27063
• ENST00000653645.1:n.437-4475G>C

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-4475G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,062 control chromosomes in the GnomAD database, including 19,092 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 0.50 (19092 hom., cov: 33)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.604 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.437-4475G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75297 AN: 151944 Hom.: 19081 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.495 AC: 75338 AN: 152062 Hom.: 19092 Cov.: 33 AF XY: 0.498 AC XY: 36981 AN XY: 74330

African (AFR) AF: 0.385 AC: 15982 AN: 41460

American (AMR) AF: 0.549 AC: 8384 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2952 AN: 5164

South Asian (SAS) AF: 0.622 AC: 3001 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5378 AN: 10568

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.537 AC: 36529 AN: 67992

Other (OTH) AF: 0.485 AC: 1024 AN: 2110

Alfa AF: 0.521 Hom.: 2670

Bravo AF: 0.493

Asia WGS AF: 0.571 AC: 1983 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	2.4
DANN	Benign	0.25
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs27063; hg19: chr5-1360125;