8-2656368-T-C

Position:

• chr8-2656368-T-C

Variant summary

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

The NR_125425.1(LINC03021):​n.238+18362A>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 0.132 in 152,090 control chromosomes in the GnomAD database, including 1,674 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 0.13 (1674 hom., cov: 32)
• Consequence: LINC03021 NR_125425.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878

Genes affected

LINC03021 (HGNC:56149): (long intergenic non-protein coding RNA 3021)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03021	NR_125425.1	n.238+18362A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03021	ENST00000654884.1	n.523-7483A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20128 AN: 151974 Hom.: 1670 Cov.: 32

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.132 AC: 20142 AN: 152090 Hom.: 1674 Cov.: 32 AF XY: 0.136 AC XY: 10142 AN XY: 74350

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.134

Alfa AF: 0.103 Hom.: 357

Bravo AF: 0.140

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9314462; hg19: chr8-2513884;