chr5-125246089-T-G

Variant names:

• chr5-125246089-T-G
• rs719829
• ENST00000647105.1:n.288-79263T>G

Variant summary

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

The ENST00000647105.1(LINC02240):​n.288-79263T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,056 control chromosomes in the GnomAD database, including 7,171 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 0.29 (7171 hom., cov: 32)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 5 publications found

Genes affected

LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

LOC101927421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927421	NR_109882.1	n.377+76463T>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-79263T>G		intron_variant	Intron 2 of 6
LINC02240	ENST00000825646.1	n.278+76463T>G		intron_variant	Intron 4 of 5
LINC02240	ENST00000825648.1	n.276+76463T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44472 AN: 151938 Hom.: 7162 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.293 AC: 44511 AN: 152056 Hom.: 7171 Cov.: 32 AF XY: 0.304 AC XY: 22563 AN XY: 74318

African (AFR) AF: 0.219 AC: 9083 AN: 41486

American (AMR) AF: 0.325 AC: 4970 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2665 AN: 5160

South Asian (SAS) AF: 0.552 AC: 2656 AN: 4814

European-Finnish (FIN) AF: 0.409 AC: 4321 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18796 AN: 67970

Other (OTH) AF: 0.294 AC: 619 AN: 2108

Alfa AF: 0.277 Hom.: 16455

Bravo AF: 0.279

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs719829; hg19: chr5-124581782;