ENST00000560675.2:n.558-769A>G

Variant names:

• chr15-38757715-T-C
• rs723049
• ENST00000560675.2:n.558-769A>G

Variant summary

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

The ENST00000560675.2(ENSG00000259731):​n.558-769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,040 control chromosomes in the GnomAD database, including 22,414 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 0.54 (22414 hom., cov: 32)
• Consequence: ENSG00000259731 ENST00000560675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 6 publications found

Genes affected

ENSG00000259731 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560675.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259731	ENST00000560675.2	TSL:3	n.558-769A>G		intron	N/A
	LINC02694	ENST00000644461.1		n.97-65283T>C		intron	N/A
	LINC02694	ENST00000645416.2		n.53-31313T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81982 AN: 151920 Hom.: 22408 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.539 AC: 82017 AN: 152040 Hom.: 22414 Cov.: 32 AF XY: 0.540 AC XY: 40137 AN XY: 74310

African (AFR) AF: 0.452 AC: 18752 AN: 41502

American (AMR) AF: 0.528 AC: 8066 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3136 AN: 5168

South Asian (SAS) AF: 0.505 AC: 2433 AN: 4822

European-Finnish (FIN) AF: 0.639 AC: 6737 AN: 10544

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.573 AC: 38900 AN: 67940

Other (OTH) AF: 0.555 AC: 1173 AN: 2114

Alfa AF: 0.563 Hom.: 19001

Bravo AF: 0.528

Asia WGS AF: 0.578 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs723049; hg19: chr15-39049916;