rs1439564

chr5-125223958-T-G

Variant summary

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

The NR_109882.1(LOC101927421):n.377+54332T>G 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 0.409 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

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

LOC101927421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927421	NR_109882.1	n.377+54332T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-101394T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.442

Alfa AF: 0.494 Hom.: 38106

Bravo AF: 0.407

Asia WGS AF: 0.228 AC: 794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.8
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439564; hg19: chr5-124559651;