8-29773426-G-T

Position:

• chr8-29773426-G-T

Variant summary

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

The NR_125815.1(LINC02099):​n.272-16906G>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 0.435 in 152,076 control chromosomes in the GnomAD database, including 17,122 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 0.44 (17122 hom., cov: 32)
• Consequence: LINC02099 NR_125815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

LINC02099 (HGNC:52953): (long intergenic non-protein coding RNA 2099)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02099	NR_125815.1	n.272-16906G>T		intron_variant, non_coding_transcript_variant
LINC02099	NR_125814.1	n.272-16906G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02099	ENST00000517491.1	n.231-16906G>T		intron_variant, non_coding_transcript_variant		1
LINC02099	ENST00000523123.5	n.256-16906G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66104 AN: 151958 Hom.: 17086 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.435 AC: 66193 AN: 152076 Hom.: 17122 Cov.: 32 AF XY: 0.431 AC XY: 32044 AN XY: 74338

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.432

Alfa AF: 0.321 Hom.: 10411

Bravo AF: 0.451

Asia WGS AF: 0.275 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.14
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6982080; hg19: chr8-29630942;