rs12903120

Variant names:

• chr15-38695896-G-T
• rs12903120
• ENST00000644461.1:n.96+67741G>T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.96+67741G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,064 control chromosomes in the GnomAD database, including 5,242 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 0.26 (5242 hom., cov: 33)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 19 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02694	ENST00000644461.1	n.96+67741G>T		intron_variant	Intron 1 of 4
LINC02694	ENST00000646232.1	n.163+6582G>T		intron_variant	Intron 2 of 3
LINC02694	ENST00000647456.1	n.572+6582G>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38783 AN: 151946 Hom.: 5242 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.255 AC: 38805 AN: 152064 Hom.: 5242 Cov.: 33 AF XY: 0.253 AC XY: 18802 AN XY: 74352

African (AFR) AF: 0.193 AC: 7999 AN: 41508

American (AMR) AF: 0.268 AC: 4099 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3466

East Asian (EAS) AF: 0.0940 AC: 487 AN: 5180

South Asian (SAS) AF: 0.207 AC: 1000 AN: 4828

European-Finnish (FIN) AF: 0.255 AC: 2687 AN: 10544

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20525 AN: 67950

Other (OTH) AF: 0.277 AC: 584 AN: 2108

Alfa AF: 0.292 Hom.: 21765

Bravo AF: 0.259

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs12903120; hg19: chr15-38988097;