rs10508509

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000295551 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.215 AC: 8937 AN: 41480

American (AMR) AF: 0.0692 AC: 1059 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3472

East Asian (EAS) AF: 0.140 AC: 727 AN: 5178

South Asian (SAS) AF: 0.0863 AC: 416 AN: 4822

European-Finnish (FIN) AF: 0.0245 AC: 259 AN: 10588

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0237 AC: 1611 AN: 68024

Other (OTH) AF: 0.0649 AC: 137 AN: 2110

Alfa AF: 0.0450 Hom.: 447

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
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10508509; hg19: chr10-16323035;