rs1351267

Variant names:

• chr3-152045912-C-T
• rs1351267
• ENST00000781911.1:n.814G>A

Variant summary

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

The ENST00000781911.1(LINC02917):​n.814G>A 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 0.453 in 151,906 control chromosomes in the GnomAD database, including 15,819 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 0.45 (15819 hom., cov: 31)
• Consequence: LINC02917 ENST00000781911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 5 publications found

Genes affected

LINC02917 (HGNC:55643): (long intergenic non-protein coding RNA 2917)

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 (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02917	ENST00000781911.1	n.814G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LINC02917	ENST00000781910.1	n.834+13G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68734 AN: 151788 Hom.: 15802 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.453 AC: 68802 AN: 151906 Hom.: 15819 Cov.: 31 AF XY: 0.462 AC XY: 34286 AN XY: 74234

African (AFR) AF: 0.449 AC: 18598 AN: 41404

American (AMR) AF: 0.502 AC: 7661 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1533 AN: 3462

East Asian (EAS) AF: 0.441 AC: 2273 AN: 5160

South Asian (SAS) AF: 0.606 AC: 2912 AN: 4808

European-Finnish (FIN) AF: 0.486 AC: 5136 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29176 AN: 67946

Other (OTH) AF: 0.435 AC: 917 AN: 2108

Alfa AF: 0.445 Hom.: 10085

Bravo AF: 0.451

Asia WGS AF: 0.516 AC: 1793 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	2.7
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1351267; hg19: chr3-151763701;