rs10499216

Variant names:

• chr6-140044134-C-T
• rs10499216
• ENST00000456896.6:n.82-23303C>T

Variant summary

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

The ENST00000456896.6(LINC02941):​n.82-23303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0158 in 152,174 control chromosomes in the GnomAD database, including 51 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 0.016 (51 hom., cov: 32)
• Consequence: LINC02941 ENST00000456896.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 2 publications found

Genes affected

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

LOC107986652 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02941	NR_121622.1	n.115-23303C>T		intron_variant	Intron 1 of 3
LINC02941	NR_121623.1	n.115-48857C>T		intron_variant	Intron 1 of 1
LOC107986652	XR_001744383.2	n.489-7510G>A		intron_variant	Intron 3 of 3
LOC107986652	XR_001744384.2	n.369-7510G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02941	ENST00000456896.6	n.82-23303C>T		intron_variant	Intron 1 of 3	5
LINC02941	ENST00000656952.2	n.82-42548C>T		intron_variant	Intron 1 of 2
LINC02941	ENST00000664620.1	n.141-42548C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0158 AC: 2397 AN: 152056 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.00278

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00839

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0158 AC: 2399 AN: 152174 Hom.: 51 Cov.: 32 AF XY: 0.0167 AC XY: 1241 AN XY: 74388

African (AFR) AF: 0.00277 AC: 115 AN: 41548

American (AMR) AF: 0.00838 AC: 128 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3464

East Asian (EAS) AF: 0.107 AC: 554 AN: 5156

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4814

European-Finnish (FIN) AF: 0.0283 AC: 300 AN: 10594

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

European-Non Finnish (NFE) AF: 0.0164 AC: 1117 AN: 68004

Other (OTH) AF: 0.0118 AC: 25 AN: 2110

Alfa AF: 0.0138 Hom.: 2

Bravo AF: 0.0143

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.42
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs10499216; hg19: chr6-140365271;