rs10169462

chr2-59225027-C-T

Variant summary

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

The NR_110219.1(LINC01793):n.67+7253C>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 0.146 in 152,084 control chromosomes in the GnomAD database, including 1,682 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 0.15 (1682 hom., cov: 32)
• Consequence: LINC01793 NR_110219.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01793	NR_110219.1	n.67+7253C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01793	ENST00000409590.1	n.67+7253C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000606382.1	n.434-6303G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22213 AN: 151966 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.146 AC: 22230 AN: 152084 Hom.: 1682 Cov.: 32 AF XY: 0.147 AC XY: 10954 AN XY: 74340

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.134

Alfa AF: 0.159 Hom.: 408

Bravo AF: 0.135

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.073
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169462; hg19: chr2-59452162;