15-53046879-T-C

Position:

• chr15-53046879-T-C

Variant summary

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

The ENST00000692805.1(LINC02490):​n.87+11623T>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 0.107 in 152,148 control chromosomes in the GnomAD database, including 1,145 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 0.11 (1145 hom., cov: 32)
• Consequence: LINC02490 ENST00000692805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

LINC02490 (HGNC:53471): (long intergenic non-protein coding RNA 2490)

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983981	XR_004837530.2	n.533+71030T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000692805.1	n.87+11623T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16216 AN: 152032 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.107 AC: 16235 AN: 152148 Hom.: 1145 Cov.: 32 AF XY: 0.111 AC XY: 8278 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0999

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0614

Gnomad4 NFE AF: 0.0578

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0774 Hom.: 138

Bravo AF: 0.112

Asia WGS AF: 0.247 AC: 856 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047668; hg19: chr15-53339076;