rs4869566

Positions:

• chr5-38129325-G-A
• chr5-38129325-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_147009.1(LINC02107):​n.234-54379G>A 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 0.737 in 152,184 control chromosomes in the GnomAD database, including 41,904 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 0.74 (41904 hom., cov: 34)
• Consequence: LINC02107 NR_147009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

Genes affected

LINC02119 (HGNC:52975): (long intergenic non-protein coding RNA 2119)

LINC02107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02107	NR_147009.1	n.234-54379G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02119	ENST00000669275.1	n.314-3118G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112139 AN: 152066 Hom.: 41873 Cov.: 34

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.737 AC: 112224 AN: 152184 Hom.: 41904 Cov.: 34 AF XY: 0.731 AC XY: 54371 AN XY: 74398

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.739

Alfa AF: 0.719 Hom.: 17885

Bravo AF: 0.747

Asia WGS AF: 0.691 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4869566; hg19: chr5-38129427;