8-2691853-T-C

Variant names:

• chr8-2691853-T-C
• rs17515
• ENST00000725447.1:n.226A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725447.1(LINC03021):​n.226A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,924 control chromosomes in the GnomAD database, including 18,164 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 0.44 (18164 hom., cov: 32)
• Consequence: LINC03021 ENST00000725447.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03021	NR_125425.1	n.123-17008A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03021	ENST00000725447.1	n.226A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC03021	ENST00000517357.6	n.163-12914A>G		intron_variant	Intron 2 of 5	4
LINC03021	ENST00000517984.6	n.273+13362A>G		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66906 AN: 151806 Hom.: 18135 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.441 AC: 66981 AN: 151924 Hom.: 18164 Cov.: 32 AF XY: 0.436 AC XY: 32351 AN XY: 74196

African (AFR) AF: 0.776 AC: 32160 AN: 41456

American (AMR) AF: 0.299 AC: 4572 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1373 AN: 5118

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4818

European-Finnish (FIN) AF: 0.331 AC: 3482 AN: 10520

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21573 AN: 67960

Other (OTH) AF: 0.431 AC: 908 AN: 2108

Alfa AF: 0.358 Hom.: 37154

Bravo AF: 0.453

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.11
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17515; hg19: chr8-2549355;