rs448669

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648275.1(LINC02646):​n.504-12212A>C variant causes a intron, non coding transcript 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 ENST00000648275.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02646	ENST00000648275.1	n.504-12212A>C		intron_variant, non_coding_transcript_variant
LINC02646	ENST00000439421.2	n.24-12212A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.229

Alfa AF: 0.186 Hom.: 1326

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs448669; hg19: chr10-132268933;