rs10509586

Variant names:

• chr10-89981680-G-T
• rs10509586
• ENST00000664430.1:n.548+66910G>T

Variant summary

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

The ENST00000664430.1(LINC00865):​n.548+66910G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,244 control chromosomes in the GnomAD database, including 616 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 0.068 (616 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 2 publications found

Genes affected

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00865	ENST00000664430.1	n.548+66910G>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000715760.1	n.741-38155G>T		intron_variant	Intron 3 of 3
LINC00865	ENST00000749371.1	n.347+66910G>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000749372.1	n.292+66910G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10327 AN: 152126 Hom.: 618 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0679 AC: 10333 AN: 152244 Hom.: 616 Cov.: 32 AF XY: 0.0639 AC XY: 4754 AN XY: 74446

African (AFR) AF: 0.151 AC: 6286 AN: 41528

American (AMR) AF: 0.0349 AC: 533 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3464

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5190

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4818

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0432 AC: 2942 AN: 68026

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0497 Hom.: 171

Bravo AF: 0.0740

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.56
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10509586; hg19: chr10-91741437;