ENST00000666064.1:n.301-18412C>A

Variant names:

• chr10-2387113-G-T
• rs826489
• ENST00000666064.1:n.301-18412C>A

Variant summary

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

The ENST00000666064.1(LINC02645):​n.301-18412C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,722 control chromosomes in the GnomAD database, including 29,009 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 0.62 (29009 hom., cov: 31)
• Consequence: LINC02645 ENST00000666064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

LINC02645 (HGNC:54129): (long intergenic non-protein coding RNA 2645)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.659 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
LINC02645	ENST00000666064.1	n.301-18412C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93317 AN: 151604 Hom.: 28985 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.615 AC: 93379 AN: 151722 Hom.: 29009 Cov.: 31 AF XY: 0.619 AC XY: 45858 AN XY: 74136

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.592

Alfa AF: 0.615 Hom.: 37602

Bravo AF: 0.611

Asia WGS AF: 0.600 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826489; hg19: chr10-2429307;