rs10490113

chr2-59272212-A-C

Variant summary

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

The NR_110219.1(LINC01793):n.168-5320A>C 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 0.119 in 152,230 control chromosomes in the GnomAD database, including 1,134 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 0.12 (1134 hom., cov: 32)
• Consequence: LINC01793 NR_110219.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

LINC01793 (HGNC:52583): (long intergenic non-protein coding RNA 1793)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01793	NR_110219.1	n.168-5320A>C		intron_variant, non_coding_transcript_variant
LOC105374754	XR_002959389.2	n.1448-22519T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01793	ENST00000409590.1	n.168-5320A>C		intron_variant, non_coding_transcript_variant		2
	ENST00000412409.3	n.546-31109T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.434-53488T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18081 AN: 152112 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.119 AC: 18096 AN: 152230 Hom.: 1134 Cov.: 32 AF XY: 0.120 AC XY: 8896 AN XY: 74420

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0308

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.106 Hom.: 1538

Bravo AF: 0.119

Asia WGS AF: 0.0880 AC: 305 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490113; hg19: chr2-59499347;