rs10508509

Variant names:

• chr10-16281036-C-T
• rs10508509
• ENST00000417542.1:n.49+2287C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417542.1(LINC02654):​n.49+2287C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,172 control chromosomes in the GnomAD database, including 1,136 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 0.088 (1136 hom., cov: 32)
• Consequence: LINC02654 ENST00000417542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

LINC02654 (HGNC:54140): (long intergenic non-protein coding RNA 2654)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02654	NR_184073.1	n.693+2287C>T		intron_variant	Intron 1 of 2
LINC02654	NR_184074.1	n.693+2287C>T		intron_variant	Intron 1 of 2
LINC02654	NR_184075.1	n.693+2287C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02654	ENST00000417542.1	n.49+2287C>T		intron_variant	Intron 1 of 3	2
LINC02654	ENST00000434386.6	n.206+2287C>T		intron_variant	Intron 2 of 3	2
LINC02654	ENST00000652949.1	n.657+2287C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13380 AN: 152054 Hom.: 1121 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0882 AC: 13424 AN: 152172 Hom.: 1136 Cov.: 32 AF XY: 0.0877 AC XY: 6523 AN XY: 74406

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.0245

Gnomad4 NFE AF: 0.0237

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0359 Hom.: 189

Bravo AF: 0.0966

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508509; hg19: chr10-16323035;