rs689771

Variant names:

• chr15-53200638-C-A
• rs689771
• ENST00000780988.1:n.309+6795C>A

Variant summary

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

The ENST00000780988.1(LINC02490):​n.309+6795C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,048 control chromosomes in the GnomAD database, including 7,406 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 (7406 hom., cov: 33)
• Consequence: LINC02490 ENST00000780988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 2 publications found

Genes affected

LINC02490 (HGNC:53471): (long intergenic non-protein coding RNA 2490)

LOC107983981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780988.1. 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
	LINC02490	ENST00000780988.1		n.309+6795C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46764 AN: 151930 Hom.: 7401 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.308 AC: 46800 AN: 152048 Hom.: 7406 Cov.: 33 AF XY: 0.317 AC XY: 23545 AN XY: 74326

African (AFR) AF: 0.257 AC: 10652 AN: 41466

American (AMR) AF: 0.384 AC: 5867 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5166

South Asian (SAS) AF: 0.342 AC: 1651 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4104 AN: 10548

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20039 AN: 67974

Other (OTH) AF: 0.304 AC: 643 AN: 2116

Alfa AF: 0.296 Hom.: 1313

Bravo AF: 0.308

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs689771;

hg19: chr15-53492835;