chr5-125223958-T-G

Variant names:

• chr5-125223958-T-G
• rs1439564
• ENST00000647105.1:n.288-101394T>G

Variant summary

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

The NR_109882.1(LOC101927421):​n.377+54332T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,996 control chromosomes in the GnomAD database, including 13,826 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 0.41 (13826 hom., cov: 32)
• Consequence: LOC101927421 NR_109882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109882.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927421	NR_109882.1		n.377+54332T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02240	ENST00000647105.1		n.288-101394T>G		intron	N/A
	LINC02240	ENST00000825646.1		n.278+54332T>G		intron	N/A
	LINC02240	ENST00000825648.1		n.276+54332T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62105 AN: 151880 Hom.: 13817 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.409 AC: 62128 AN: 151996 Hom.: 13826 Cov.: 32 AF XY: 0.400 AC XY: 29731 AN XY: 74286

African (AFR) AF: 0.278 AC: 11510 AN: 41472

American (AMR) AF: 0.405 AC: 6189 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3470

East Asian (EAS) AF: 0.145 AC: 746 AN: 5162

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4814

European-Finnish (FIN) AF: 0.381 AC: 4026 AN: 10554

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34794 AN: 67938

Other (OTH) AF: 0.442 AC: 936 AN: 2116

Alfa AF: 0.481 Hom.: 75451

Bravo AF: 0.407

Asia WGS AF: 0.228 AC: 794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.80
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1439564; hg19: chr5-124559651;