rs270584

Positions:

• chr5-38074752-C-A
• chr5-38074752-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+45696C>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 0.534 in 152,068 control chromosomes in the GnomAD database, including 25,305 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 0.53 (25305 hom., cov: 32)
• Consequence: LINC02107 NR_147009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+45696C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02119	ENST00000669275.1	n.313+45696C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81169 AN: 151950 Hom.: 25247 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.534 AC: 81278 AN: 152068 Hom.: 25305 Cov.: 32 AF XY: 0.533 AC XY: 39617 AN XY: 74334

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.440

Alfa AF: 0.414 Hom.: 13844

Bravo AF: 0.535

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs270584; hg19: chr5-38074854;