chr15-38720378-C-T

Variant names:

• chr15-38720378-C-T
• rs8024474
• ENST00000644461.1:n.96+92223C>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+92223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,120 control chromosomes in the GnomAD database, including 7,797 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 0.31 (7797 hom., cov: 33)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 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+92223C>T		intron	N/A
	LINC02694	ENST00000645416.2		n.52+17454C>T		intron	N/A
	LINC02694	ENST00000645994.2		n.256-12858C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47351 AN: 152004 Hom.: 7810 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.311 AC: 47355 AN: 152120 Hom.: 7797 Cov.: 33 AF XY: 0.316 AC XY: 23490 AN XY: 74370

African (AFR) AF: 0.223 AC: 9262 AN: 41508

American (AMR) AF: 0.372 AC: 5690 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2901 AN: 5166

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4818

European-Finnish (FIN) AF: 0.286 AC: 3034 AN: 10590

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21746 AN: 67968

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.315 Hom.: 24338

Bravo AF: 0.311

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs8024474; hg19: chr15-39012579;