rs10518700

Variant names:

• chr15-52922950-C-T
• rs10518700
• ENST00000780970.1:n.196+6511C>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.196+6511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,234 control chromosomes in the GnomAD database, including 387 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 (387 hom., cov: 32)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837529.2	n.194+6511C>T		intron_variant	Intron 2 of 4
LOC107983981	XR_004837530.2	n.247+6511C>T		intron_variant	Intron 3 of 5
LOC107983981	XR_004837531.2	n.194+6511C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.196+6511C>T		intron_variant	Intron 2 of 5
LINC02490	ENST00000780971.1	n.309+6511C>T		intron_variant	Intron 3 of 6
LINC02490	ENST00000780972.1	n.231+6511C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7731 AN: 152116 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0509 AC: 7748 AN: 152234 Hom.: 387 Cov.: 32 AF XY: 0.0512 AC XY: 3812 AN XY: 74434

African (AFR) AF: 0.109 AC: 4522 AN: 41524

American (AMR) AF: 0.0775 AC: 1186 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3472

East Asian (EAS) AF: 0.185 AC: 959 AN: 5176

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4824

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0102 AC: 697 AN: 68014

Other (OTH) AF: 0.0526 AC: 111 AN: 2112

Alfa AF: 0.0465 Hom.: 61

Bravo AF: 0.0622

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10518700; hg19: chr15-53215147;