rs10091374

chr8-70474669-T-Achr8-70474669-T-C

Variant summary

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

The NR_110653.1(LINC03020):n.712+2824T>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 0.466 in 151,854 control chromosomes in the GnomAD database, including 16,888 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 0.47 (16888 hom., cov: 31)
• Consequence: LINC03020 NR_110653.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

LINC03020 (HGNC:56148): (long intergenic non-protein coding RNA 3020)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03020	NR_110653.1	n.712+2824T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03020	ENST00000520259.1	n.712+2824T>A		intron_variant, non_coding_transcript_variant		2
	ENST00000521051.1	n.704-3525A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70702 AN: 151736 Hom.: 16855 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.466 AC: 70794 AN: 151854 Hom.: 16888 Cov.: 31 AF XY: 0.464 AC XY: 34449 AN XY: 74222

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.457

Alfa AF: 0.478 Hom.: 2154

Bravo AF: 0.458

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10091374; hg19: chr8-71386904;