rs2296465

Variant names:

• chr10-3267455-A-G
• rs2296465
• ENST00000724808.1:n.247+9532T>C

Variant summary

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

The ENST00000724808.1(LINC02668):​n.247+9532T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,022 control chromosomes in the GnomAD database, including 4,988 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 0.25 (4988 hom., cov: 32)
• Consequence: LINC02668 ENST00000724808.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 1 publications found

Genes affected

LINC02668 (HGNC:54154): (long intergenic non-protein coding RNA 2668)

ENSG00000227338 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.393 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
LINC02668	ENST00000724808.1	n.247+9532T>C		intron_variant	Intron 1 of 1
LINC02668	ENST00000724809.1	n.204+9532T>C		intron_variant	Intron 1 of 2
ENSG00000227338	ENST00000436340.2	n.*239A>G		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37861 AN: 151902 Hom.: 4980 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.249 AC: 37891 AN: 152022 Hom.: 4988 Cov.: 32 AF XY: 0.257 AC XY: 19085 AN XY: 74330

African (AFR) AF: 0.174 AC: 7208 AN: 41482

American (AMR) AF: 0.322 AC: 4914 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1358 AN: 5174

South Asian (SAS) AF: 0.408 AC: 1960 AN: 4808

European-Finnish (FIN) AF: 0.332 AC: 3505 AN: 10548

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17473 AN: 67958

Other (OTH) AF: 0.228 AC: 480 AN: 2106

Alfa AF: 0.253 Hom.: 8670

Bravo AF: 0.243

Asia WGS AF: 0.349 AC: 1215 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	1.4
DANN	Benign	0.33
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2296465; hg19: chr10-3309647;