2-8132890-G-C

Position:

• chr2-8132890-G-C

Variant summary

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

The NR_034135.1(LINC00299):​n.954-72485C>G 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 0.871 in 152,290 control chromosomes in the GnomAD database, including 58,517 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 0.87 (58517 hom., cov: 34)
• Consequence: LINC00299 NR_034135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

LINC00298 (HGNC:49257): (long intergenic non-protein coding RNA 298)

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 = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00299	NR_034135.1	n.954-72485C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00299	ENST00000430192.5	n.714-72485C>G		intron_variant, non_coding_transcript_variant		1
LINC00298	ENST00000663636.1	n.448+144849C>G		intron_variant, non_coding_transcript_variant
LINC00298	ENST00000456681.1	n.346+144849C>G		intron_variant, non_coding_transcript_variant		3
LINC00299	ENST00000657310.1	n.356-72485C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132565 AN: 152172 Hom.: 58477 Cov.: 34

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.871 AC: 132652 AN: 152290 Hom.: 58517 Cov.: 34 AF XY: 0.865 AC XY: 64411 AN XY: 74460

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.862

Alfa AF: 0.875 Hom.: 6831

Bravo AF: 0.858

Asia WGS AF: 0.697 AC: 2423 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	4.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181130; hg19: chr2-8273020;