5-15207207-G-A

Position:

• chr5-15207207-G-A

Variant summary

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

The NR_109944.1(LINC02149):​n.267-14758C>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 0.0189 in 152,258 control chromosomes in the GnomAD database, including 96 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 0.019 (96 hom., cov: 32)
• Consequence: LINC02149 NR_109944.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

LINC02149 (HGNC:53010): (long intergenic non-protein coding RNA 2149)

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 (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02149	NR_109944.1	n.267-14758C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02149	ENST00000511443.1	n.248-14758C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2877 AN: 152140 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00454

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0189 AC: 2872 AN: 152258 Hom.: 96 Cov.: 32 AF XY: 0.0193 AC XY: 1434 AN XY: 74434

Gnomad4 AFR AF: 0.00452

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0289

Gnomad4 FIN AF: 0.00810

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00559 Hom.: 0

Bravo AF: 0.0202

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513203; hg19: chr5-15207316;