rs716188

Variant names:

• chr15-52952680-C-T
• rs716188
• ENST00000780970.1:n.197-18723C>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.197-18723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 152,282 control chromosomes in the GnomAD database, including 390 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 0.051 (390 hom., cov: 33)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837529.2	n.195-18723C>T		intron_variant	Intron 2 of 4
LOC107983981	XR_004837530.2	n.248-18723C>T		intron_variant	Intron 3 of 5
LOC107983981	XR_004837531.2	n.195-18723C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.197-18723C>T		intron_variant	Intron 2 of 5
LINC02490	ENST00000780971.1	n.310-18723C>T		intron_variant	Intron 3 of 6
LINC02490	ENST00000780972.1	n.232-18723C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7773 AN: 152164 Hom.: 390 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0511 AC: 7788 AN: 152282 Hom.: 390 Cov.: 33 AF XY: 0.0515 AC XY: 3832 AN XY: 74466

African (AFR) AF: 0.110 AC: 4572 AN: 41536

American (AMR) AF: 0.0779 AC: 1191 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.185 AC: 960 AN: 5188

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4826

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 688 AN: 68026

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0406 Hom.: 41

Bravo AF: 0.0626

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs716188; hg19: chr15-53244877;