rs10499215

chr6-139991455-C-T

Variant summary

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

The NR_121622.1(LINC02941):n.114+15023C>T 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 0.0645 in 152,042 control chromosomes in the GnomAD database, including 415 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 0.064 (415 hom., cov: 32)
• Consequence: LINC02941 NR_121622.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

LINC02941 (HGNC:55956): (long intergenic non-protein coding RNA 2941)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02941	NR_121622.1	n.114+15023C>T		intron_variant, non_coding_transcript_variant
LINC02941	NR_121623.1	n.114+15023C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02941	ENST00000456896.6	n.81+15023C>T		intron_variant, non_coding_transcript_variant		5
LINC02941	ENST00000656952.1	n.69+13028C>T		intron_variant, non_coding_transcript_variant
LINC02941	ENST00000664620.1	n.140+13028C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9795 AN: 151926 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0645 AC: 9800 AN: 152042 Hom.: 415 Cov.: 32 AF XY: 0.0660 AC XY: 4903 AN XY: 74294

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0474

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0885

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0808 Hom.: 119

Bravo AF: 0.0586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499215; hg19: chr6-140312592;