rs1494645

chr5-38083680-C-T

Variant summary

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

The NR_147009.1(LINC02107):n.233+54624C>T 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 0.149 in 152,124 control chromosomes in the GnomAD database, including 1,733 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 0.15 (1733 hom., cov: 32)
• Consequence: LINC02107 NR_147009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

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

LINC02107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02107	NR_147009.1	n.233+54624C>T		intron_variant, non_coding_transcript_variant
LOC105374730	XR_925927.3	n.159+510G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02119	ENST00000669275.1	n.314-48763C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22651 AN: 152006 Hom.: 1731 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.149 AC: 22679 AN: 152124 Hom.: 1733 Cov.: 32 AF XY: 0.151 AC XY: 11211 AN XY: 74364

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.128

Alfa AF: 0.138 Hom.: 2985

Bravo AF: 0.143

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.6
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494645; hg19: chr5-38083782;