rs9327361

chr5-125560875-A-C

Variant summary

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

The NR_109887.1(LINC02240):n.325-40341A>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 0.0586 in 152,206 control chromosomes in the GnomAD database, including 524 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 0.059 (524 hom., cov: 32)
• Consequence: LINC02240 NR_109887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02240	NR_109887.1	n.325-40341A>C		intron_variant, non_coding_transcript_variant
LOC124901056	XR_007058919.1	n.2257+51128T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.549-22672A>C		intron_variant, non_coding_transcript_variant
	ENST00000651821.1	n.325-40341A>C		intron_variant, non_coding_transcript_variant
	ENST00000651847.1	n.1076+51128T>G		intron_variant, non_coding_transcript_variant
LINC02240	ENST00000564199.1	n.325-40341A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0585 AC: 8892 AN: 152088 Hom.: 522 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0586 AC: 8925 AN: 152206 Hom.: 524 Cov.: 32 AF XY: 0.0566 AC XY: 4213 AN XY: 74424

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.00820

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0239 Hom.: 132

Bravo AF: 0.0665

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.19
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327361; hg19: chr5-124896568;