rs493218

Variant names:

• chr15-53198065-T-C
• rs493218
• ENST00000780988.1:n.309+4222T>C

Variant summary

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

The ENST00000780988.1(LINC02490):​n.309+4222T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,170 control chromosomes in the GnomAD database, including 2,211 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 0.15 (2211 hom., cov: 32)
• Consequence: LINC02490 ENST00000780988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-23361T>C		intron_variant	Intron 4 of 4
LOC107983981	XR_932257.3	n.696+4222T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780988.1	n.309+4222T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23350 AN: 152050 Hom.: 2200 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.154 AC: 23379 AN: 152170 Hom.: 2211 Cov.: 32 AF XY: 0.155 AC XY: 11500 AN XY: 74390

African (AFR) AF: 0.213 AC: 8828 AN: 41480

American (AMR) AF: 0.163 AC: 2499 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5158

South Asian (SAS) AF: 0.227 AC: 1091 AN: 4816

European-Finnish (FIN) AF: 0.0573 AC: 608 AN: 10614

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7111 AN: 68010

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.123 Hom.: 675

Bravo AF: 0.167

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs493218; hg19: chr15-53490262;