10-2390072-T-C

Variant names:

• chr10-2390072-T-C
• rs7895038
• ENST00000666064.1:n.301-21371A>G

Variant summary

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

The ENST00000666064.1(LINC02645):​n.301-21371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,072 control chromosomes in the GnomAD database, including 21,494 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 0.53 (21494 hom., cov: 33)
• Consequence: LINC02645 ENST00000666064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 3 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 = 0.598 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.301-21371A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80293 AN: 151954 Hom.: 21456 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.529 AC: 80389 AN: 152072 Hom.: 21494 Cov.: 33 AF XY: 0.527 AC XY: 39175 AN XY: 74336

African (AFR) AF: 0.554 AC: 22967 AN: 41456

American (AMR) AF: 0.483 AC: 7389 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5174

South Asian (SAS) AF: 0.617 AC: 2975 AN: 4824

European-Finnish (FIN) AF: 0.457 AC: 4826 AN: 10560

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36298 AN: 67986

Other (OTH) AF: 0.534 AC: 1126 AN: 2108

Alfa AF: 0.534 Hom.: 81190

Bravo AF: 0.529

Asia WGS AF: 0.513 AC: 1785 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	0.10
DANN	Benign	0.36
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7895038; hg19: chr10-2432266;