rs12872043

Positions:

• chr13-55114111-G-A

Variant summary

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

The ENST00000616578.1(LINC02335):​n.125+7275G>A 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 0.269 in 151,984 control chromosomes in the GnomAD database, including 5,750 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 0.27 (5750 hom., cov: 32)
• Consequence: LINC02335 ENST00000616578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

Genes affected

LINC02335 (HGNC:53255): (long intergenic non-protein coding RNA 2335)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02335	ENST00000616578.1	n.125+7275G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40806 AN: 151866 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.269 AC: 40815 AN: 151984 Hom.: 5750 Cov.: 32 AF XY: 0.272 AC XY: 20182 AN XY: 74288

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.295

Alfa AF: 0.283 Hom.: 2917

Bravo AF: 0.266

Asia WGS AF: 0.382 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
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: rs12872043; hg19: chr13-55688246;