10-2379997-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666064.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02645	ENST00000666064.1		n.301-11296A>G		intron	N/A

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

African (AFR) AF: 0.811 AC: 33534 AN: 41372

American (AMR) AF: 0.707 AC: 10783 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2067 AN: 3464

East Asian (EAS) AF: 0.734 AC: 3771 AN: 5138

South Asian (SAS) AF: 0.597 AC: 2869 AN: 4804

European-Finnish (FIN) AF: 0.725 AC: 7635 AN: 10526

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43977 AN: 67940

Other (OTH) AF: 0.667 AC: 1402 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.10
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs826470; hg19: chr10-2422191;