chr10-8282926-T-C

Variant names:

• chr10-8282926-T-C
• rs11255615
• ENST00000845990.1:n.1264-1783A>G

Variant summary

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

The ENST00000845990.1(LINC00708):​n.1264-1783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,212 control chromosomes in the GnomAD database, including 1,165 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 0.056 (1165 hom., cov: 32)
• Consequence: LINC00708 ENST00000845990.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 4 publications found

Genes affected

LINC00708 (HGNC:44694): (long intergenic non-protein coding RNA 708)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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
LINC00708	ENST00000845990.1	n.1264-1783A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8535 AN: 152094 Hom.: 1157 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00400

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0562 AC: 8553 AN: 152212 Hom.: 1165 Cov.: 32 AF XY: 0.0622 AC XY: 4631 AN XY: 74424

African (AFR) AF: 0.0392 AC: 1631 AN: 41556

American (AMR) AF: 0.206 AC: 3150 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2459 AN: 5112

South Asian (SAS) AF: 0.0819 AC: 395 AN: 4824

European-Finnish (FIN) AF: 0.0441 AC: 468 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00398 AC: 271 AN: 68030

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

Alfa AF: 0.0282 Hom.: 2362

Bravo AF: 0.0747

Asia WGS AF: 0.212 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.050
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11255615; hg19: chr10-8324889;