10-89981179-C-T

Variant names:

• chr10-89981179-C-T
• rs17129662
• ENST00000664430.1:n.548+66409C>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+66409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 149,570 control chromosomes in the GnomAD database, including 777 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 0.075 (777 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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+66409C>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000715760.1	n.741-38656C>T		intron_variant	Intron 3 of 3
LINC00865	ENST00000749371.1	n.347+66409C>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000749372.1	n.292+66409C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11251 AN: 149510 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0830

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0477

Gnomad EAS AF: 0.00335

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0387

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0753 AC: 11263 AN: 149570 Hom.: 777 Cov.: 32 AF XY: 0.0711 AC XY: 5182 AN XY: 72856

African (AFR) AF: 0.177 AC: 7188 AN: 40580

American (AMR) AF: 0.0371 AC: 560 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.0477 AC: 165 AN: 3462

East Asian (EAS) AF: 0.00355 AC: 18 AN: 5066

South Asian (SAS) AF: 0.0119 AC: 56 AN: 4720

European-Finnish (FIN) AF: 0.0133 AC: 130 AN: 9790

Middle Eastern (MID) AF: 0.0313 AC: 9 AN: 288

European-Non Finnish (NFE) AF: 0.0436 AC: 2946 AN: 67592

Other (OTH) AF: 0.0559 AC: 116 AN: 2076

Alfa AF: 0.0520 Hom.: 1191

Bravo AF: 0.0824

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs17129662; hg19: chr10-91740936;