10-2382362-C-T

Variant names:

• chr10-2382362-C-T
• rs12571964
• ENST00000666064.1:n.301-13661G>A

Variant summary

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

The ENST00000666064.1(LINC02645):​n.301-13661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,108 control chromosomes in the GnomAD database, including 2,406 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 0.17 (2406 hom., cov: 32)
• Consequence: LINC02645 ENST00000666064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02645	ENST00000666064.1		n.301-13661G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26415 AN: 151988 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.174 AC: 26464 AN: 152108 Hom.: 2406 Cov.: 32 AF XY: 0.175 AC XY: 13013 AN XY: 74336

African (AFR) AF: 0.164 AC: 6811 AN: 41506

American (AMR) AF: 0.173 AC: 2650 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3470

East Asian (EAS) AF: 0.0891 AC: 460 AN: 5160

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4814

European-Finnish (FIN) AF: 0.174 AC: 1837 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12402 AN: 67984

Other (OTH) AF: 0.164 AC: 347 AN: 2110

Alfa AF: 0.179 Hom.: 6871

Bravo AF: 0.173

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		0.015

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12571964;

hg19: chr10-2424556;