10-2379997-T-C

Variant names:

• chr10-2379997-T-C
• rs826470
• ENST00000666064.1:n.301-11296A>G

Variant summary

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

The ENST00000666064.1(LINC02645):​n.301-11296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,804 control chromosomes in the GnomAD database, including 38,052 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 0.70 (38052 hom., cov: 29)
• Consequence: LINC02645 ENST00000666064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 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.301-11296A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106524 AN: 151686 Hom.: 38017 Cov.: 29

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.702 AC: 106612 AN: 151804 Hom.: 38052 Cov.: 29 AF XY: 0.703 AC XY: 52132 AN XY: 74192

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.667

Alfa AF: 0.662 Hom.: 9279

Bravo AF: 0.708

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826470; hg19: chr10-2422191;