rs1439568

Positions:

• chr5-125210039-T-C

Variant summary

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

The NR_109882.1(LOC101927421):​n.377+40413T>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 0.407 in 152,122 control chromosomes in the GnomAD database, including 13,016 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 (13016 hom., cov: 33)
• Consequence: LOC101927421 NR_109882.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927421	NR_109882.1	n.377+40413T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-115313T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61821 AN: 152004 Hom.: 12999 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.407 AC: 61879 AN: 152122 Hom.: 13016 Cov.: 33 AF XY: 0.406 AC XY: 30189 AN XY: 74380

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.0872

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.390

Alfa AF: 0.411 Hom.: 17806

Bravo AF: 0.395

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439568; hg19: chr5-124545732;