rs448669

Variant names:

• chr10-130470669-A-C
• rs448669
• ENST00000439421.2:n.24-12212A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-130470669-A-C
• chr10-130470669-A-T

Variant summary

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

The ENST00000439421.2(LINC02646):​n.24-12212A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,174 control chromosomes in the GnomAD database, including 5,013 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 0.24 (5013 hom., cov: 33)
• Consequence: LINC02646 ENST00000439421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

LINC02646 (HGNC:54130): (long intergenic non-protein coding RNA 2646)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 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
LINC02646	ENST00000439421.2	n.24-12212A>C		intron_variant	Intron 1 of 1	3
LINC02646	ENST00000648275.1	n.504-12212A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36417 AN: 152056 Hom.: 5002 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.240 AC: 36455 AN: 152174 Hom.: 5013 Cov.: 33 AF XY: 0.243 AC XY: 18087 AN XY: 74404

African (AFR) AF: 0.314 AC: 13015 AN: 41506

American (AMR) AF: 0.288 AC: 4395 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.546 AC: 2825 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1179 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2092 AN: 10594

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11738 AN: 68012

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.186 Hom.: 1474

Bravo AF: 0.251

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs448669; hg19: chr10-132268933;