rs7826304

Positions:

• chr8-46867313-C-A
• chr8-46867313-C-G
• chr8-46867313-C-T

Variant summary

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

The ENST00000659403.1(LINC00293):​n.364+16570C>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 0.732 in 152,022 control chromosomes in the GnomAD database, including 40,865 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 0.73 (40865 hom., cov: 31)
• Consequence: LINC00293 ENST00000659403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

LINC00293 (HGNC:39078): (long intergenic non-protein coding RNA 293)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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
LINC00293	ENST00000659403.1	n.364+16570C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111160 AN: 151904 Hom.: 40825 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.732 AC: 111258 AN: 152022 Hom.: 40865 Cov.: 31 AF XY: 0.728 AC XY: 54084 AN XY: 74284

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.738

Alfa AF: 0.668 Hom.: 3065

Bravo AF: 0.747

Asia WGS AF: 0.722 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7826304; hg19: chr8-47778935;