rs12899449

chr15-38703290-A-G

Variant summary

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

The ENST00000644461.1(LINC02694):n.96+75135A>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 0.237 in 152,184 control chromosomes in the GnomAD database, including 4,693 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 0.24 (4693 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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
LINC02694	ENST00000644461.1	n.96+75135A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36089 AN: 152066 Hom.: 4692 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.237 AC: 36102 AN: 152184 Hom.: 4693 Cov.: 32 AF XY: 0.234 AC XY: 17424 AN XY: 74416

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.265

Alfa AF: 0.275 Hom.: 7225

Bravo AF: 0.240

Asia WGS AF: 0.125 AC: 435 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.6
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12899449; hg19: chr15-38995491;