chr15-38703290-A-G

Variant names:

• chr15-38703290-A-G
• rs12899449
• ENST00000644461.1:n.96+75135A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644461.1(LINC02694):​n.96+75135A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644461.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02694	ENST00000644461.1		n.96+75135A>G		intron	N/A
	LINC02694	ENST00000645416.2		n.52+366A>G		intron	N/A
	LINC02694	ENST00000645994.2		n.255+6551A>G		intron	N/A

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

African (AFR) AF: 0.169 AC: 7038 AN: 41542

American (AMR) AF: 0.253 AC: 3862 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3470

East Asian (EAS) AF: 0.0290 AC: 150 AN: 5180

South Asian (SAS) AF: 0.193 AC: 930 AN: 4826

European-Finnish (FIN) AF: 0.238 AC: 2524 AN: 10596

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19593 AN: 67964

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.273 Hom.: 18293

Bravo AF: 0.240

Asia WGS AF: 0.125 AC: 435 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12899449; hg19: chr15-38995491;