2-8390126-G-A

Position:

• chr2-8390126-G-A

Variant summary

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

The ENST00000655671.1(LINC00299):​n.444+1827C>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 0.348 in 152,014 control chromosomes in the GnomAD database, including 9,728 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 0.35 (9728 hom., cov: 31)
• Consequence: LINC00299 ENST00000655671.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000655671.1	n.444+1827C>T		intron_variant, non_coding_transcript_variant
LINC00299	ENST00000661371.1	n.485+1827C>T		intron_variant, non_coding_transcript_variant
LINC00299	ENST00000669954.1	n.571+1827C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52857 AN: 151896 Hom.: 9723 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.348 AC: 52896 AN: 152014 Hom.: 9728 Cov.: 31 AF XY: 0.355 AC XY: 26348 AN XY: 74310

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.329

Alfa AF: 0.371 Hom.: 10507

Bravo AF: 0.333

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13008689; hg19: chr2-8530256;