rs933399

Positions:

• chr12-111369695-G-A
• chr12-111369695-G-C
• chr12-111369695-G-T

Variant summary

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

The ENST00000552663.2(LINC02356):​n.60+375G>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 0.421 in 151,920 control chromosomes in the GnomAD database, including 17,642 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 0.42 (17642 hom., cov: 31)
• Consequence: LINC02356 ENST00000552663.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

LINC02356 (HGNC:53278): (long intergenic non-protein coding RNA 2356)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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
LINC02356	ENST00000552663.2	n.60+375G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63869 AN: 151804 Hom.: 17600 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.421 AC: 63979 AN: 151920 Hom.: 17642 Cov.: 31 AF XY: 0.427 AC XY: 31662 AN XY: 74230

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.401

Alfa AF: 0.279 Hom.: 6745

Bravo AF: 0.452

Asia WGS AF: 0.691 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933399; hg19: chr12-111807499;