rs11258317

Variant names:

• chr10-6365775-G-A
• rs11258317
• ENST00000783921.1:n.405+20995G>A

Variant summary

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

The ENST00000783921.1(LINC02649):​n.405+20995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,044 control chromosomes in the GnomAD database, including 8,354 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 0.32 (8354 hom., cov: 32)
• Consequence: LINC02649 ENST00000783921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 7 publications found

Genes affected

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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
LINC02649	ENST00000783921.1	n.405+20995G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48632 AN: 151926 Hom.: 8352 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.320 AC: 48662 AN: 152044 Hom.: 8354 Cov.: 32 AF XY: 0.320 AC XY: 23766 AN XY: 74318

African (AFR) AF: 0.244 AC: 10112 AN: 41468

American (AMR) AF: 0.283 AC: 4331 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3472

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5186

South Asian (SAS) AF: 0.273 AC: 1311 AN: 4810

European-Finnish (FIN) AF: 0.426 AC: 4490 AN: 10544

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26050 AN: 67964

Other (OTH) AF: 0.326 AC: 689 AN: 2114

Alfa AF: 0.351 Hom.: 25266

Bravo AF: 0.304

Asia WGS AF: 0.148 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.33
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11258317; hg19: chr10-6407737;