chr8-65551243-G-T

Position:

• chr8-65551243-G-T

Variant summary

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

The NR_033893.1(LINC01299):​n.61+11363C>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 0.713 in 151,900 control chromosomes in the GnomAD database, including 40,935 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 0.71 (40935 hom., cov: 32)
• Consequence: LINC01299 NR_033893.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

LINC01299 (HGNC:27839): (long intergenic non-protein coding RNA 1299)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01299	NR_033893.1	n.61+11363C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01299	ENST00000520902.2	n.176+11363C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108258 AN: 151782 Hom.: 40892 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.713 AC: 108363 AN: 151900 Hom.: 40935 Cov.: 32 AF XY: 0.695 AC XY: 51599 AN XY: 74218

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.695

Alfa AF: 0.709 Hom.: 23856

Bravo AF: 0.720

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6981992; hg19: chr8-66463478;