rs510115

chr4-149204319-T-C

Variant summary

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

The NR_125887.1(LINC02355):n.1053+167T>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 0.353 in 151,860 control chromosomes in the GnomAD database, including 11,537 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 0.35 (11537 hom., cov: 32)
• Consequence: LINC02355 NR_125887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

LINC02355 (HGNC:53277): (long intergenic non-protein coding RNA 2355)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02355	NR_125887.1	n.1053+167T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02355	ENST00000503100.1	n.1053+167T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53559 AN: 151742 Hom.: 11536 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.353 AC: 53558 AN: 151860 Hom.: 11537 Cov.: 32 AF XY: 0.349 AC XY: 25874 AN XY: 74216

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.372

Alfa AF: 0.404 Hom.: 2386

Bravo AF: 0.332

Asia WGS AF: 0.280 AC: 971 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.0
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs510115; hg19: chr4-150125471;