rs11959018

chr5-18712250-T-Achr5-18712250-T-C

Variant summary

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

The ENST00000512978.1(LINC02100):n.177-7756A>T 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 0.227 in 152,082 control chromosomes in the GnomAD database, including 4,233 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 0.23 (4233 hom., cov: 32)
• Consequence: LINC02100 ENST00000512978.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

Genes affected

LINC02100 (HGNC:52955): (long intergenic non-protein coding RNA 2100)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 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
LINC02100	ENST00000512978.1	n.177-7756A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34552 AN: 151966 Hom.: 4227 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.227 AC: 34576 AN: 152082 Hom.: 4233 Cov.: 32 AF XY: 0.228 AC XY: 16927 AN XY: 74354

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.226

Alfa AF: 0.0870 Hom.: 116

Bravo AF: 0.239

Asia WGS AF: 0.256 AC: 892 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11959018; hg19: chr5-18712359;