rs10499215

Variant names:

• chr6-139991455-C-T
• rs10499215
• ENST00000456896.6:n.81+15023C>T

Variant summary

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

The ENST00000456896.6(LINC02941):​n.81+15023C>T variant causes a intron 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 ENST00000456896.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 0 publications found

Genes affected

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

LOC103352541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02941	NR_121622.1	n.114+15023C>T		intron_variant	Intron 1 of 3
LINC02941	NR_121623.1	n.114+15023C>T		intron_variant	Intron 1 of 1
LOC103352541	NR_121624.1	n.-194G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02941	ENST00000456896.6	n.81+15023C>T		intron_variant	Intron 1 of 3	5
LINC02941	ENST00000656952.2	n.81+13028C>T		intron_variant	Intron 1 of 2
LINC02941	ENST00000664620.1	n.140+13028C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0158 AC: 655 AN: 41492

American (AMR) AF: 0.0871 AC: 1331 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5154

South Asian (SAS) AF: 0.0474 AC: 228 AN: 4812

European-Finnish (FIN) AF: 0.109 AC: 1150 AN: 10528

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0885 AC: 6014 AN: 67982

Other (OTH) AF: 0.0536 AC: 113 AN: 2108

Alfa AF: 0.0601 Hom.: 127

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10499215; hg19: chr6-140312592;