rs10499216

chr6-140044134-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.115-23303C>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 0.0158 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 NR_121622.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

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

LOC107986652 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02941	NR_121622.1	n.115-23303C>T		intron_variant, non_coding_transcript_variant
LOC107986652	XR_001744384.2	n.369-7510G>A		intron_variant, non_coding_transcript_variant
LINC02941	NR_121623.1	n.115-48857C>T		intron_variant, non_coding_transcript_variant
LOC107986652	XR_001744383.2	n.489-7510G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02941	ENST00000456896.6	n.82-23303C>T		intron_variant, non_coding_transcript_variant		5
LINC02941	ENST00000656952.1	n.70-42548C>T		intron_variant, non_coding_transcript_variant
LINC02941	ENST00000664620.1	n.141-42548C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00277

Gnomad4 AMR AF: 0.00838

Gnomad4 ASJ AF: 0.0113

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0283

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0118

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499216; hg19: chr6-140365271;