rs2047668

Variant names:

• chr15-53046879-T-C
• rs2047668
• ENST00000692805.2:n.93+11623T>C

Variant summary

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

The ENST00000692805.2(LINC02490):​n.93+11623T>C variant causes a intron 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 ENST00000692805.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 0 publications found

Genes affected

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

LOC107983981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107983981	XR_001751548.2	n.553+71030T>C		intron_variant	Intron 3 of 3
LOC107983981	XR_004837530.2	n.533+71030T>C		intron_variant	Intron 5 of 5
LOC107983981	XR_004837531.2	n.480+71030T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000692805.2	n.93+11623T>C		intron_variant	Intron 1 of 1
LINC02490	ENST00000780970.1	n.482+71030T>C		intron_variant	Intron 4 of 5
LINC02490	ENST00000780971.1	n.858+64481T>C		intron_variant	Intron 6 of 6

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

African (AFR) AF: 0.161 AC: 6704 AN: 41526

American (AMR) AF: 0.120 AC: 1826 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 347 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1477 AN: 5148

South Asian (SAS) AF: 0.208 AC: 999 AN: 4814

European-Finnish (FIN) AF: 0.0614 AC: 651 AN: 10610

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0578 AC: 3927 AN: 67996

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.0793 Hom.: 144

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2047668; hg19: chr15-53339076;