5-125561596-T-C

Variant summary

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

The NR_109887.1(LINC02240):n.325-39620T>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 0.0564 in 152,270 control chromosomes in the GnomAD database, including 483 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 0.056 (483 hom., cov: 32)
• Consequence: LINC02240 NR_109887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02240	NR_109887.1	n.325-39620T>C		intron_variant, non_coding_transcript_variant
LOC124901056	XR_007058919.1	n.2257+50407A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.549-21951T>C		intron_variant, non_coding_transcript_variant
	ENST00000651821.1	n.325-39620T>C		intron_variant, non_coding_transcript_variant
	ENST00000651847.1	n.1076+50407A>G		intron_variant, non_coding_transcript_variant
LINC02240	ENST00000564199.1	n.325-39620T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8566 AN: 152152 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.00838

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0564 AC: 8587 AN: 152270 Hom.: 483 Cov.: 32 AF XY: 0.0543 AC XY: 4046 AN XY: 74462

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0537

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.00838

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0354

Alfa AF: 0.00592 Hom.: 1

Bravo AF: 0.0638

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.2
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519822; hg19: chr5-124897289;