5-6599109-A-G

Position:

• chr5-6599109-A-G

Variant summary

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

The ENST00000661215.1(LINC01018):​n.757-1012A>G 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 0.448 in 152,068 control chromosomes in the GnomAD database, including 15,627 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 0.45 (15624 hom., cov: 33)
  • Exomes 𝑓: 0.64 (3 hom.)
• Consequence: LINC01018 ENST00000661215.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

LINC01018 (HGNC:27394): (long intergenic non-protein coding RNA 1018)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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
LINC01018	ENST00000661215.1	n.757-1012A>G		intron_variant, non_coding_transcript_variant
LINC01018	ENST00000669289.1	n.571-1012A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68169 AN: 151936 Hom.: 15629 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.409

GnomAD4 exome AF: 0.643 AC: 9 AN: 14 Hom.: 3 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.448 AC: 68191 AN: 152054 Hom.: 15624 Cov.: 33 AF XY: 0.456 AC XY: 33899 AN XY: 74322

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.408

Alfa AF: 0.430 Hom.: 28034

Bravo AF: 0.440

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6876835; hg19: chr5-6599222;