rs1959947

Variant names:

• chr14-41054257-A-G
• rs1959947
• ENST00000651006.2:n.642+79867A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-41054257-A-G
• chr14-41054257-A-T

Variant summary

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

The ENST00000651006.2(LINC02315):​n.642+79867A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,712 control chromosomes in the GnomAD database, including 28,275 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 0.58 (28275 hom., cov: 31)
• Consequence: LINC02315 ENST00000651006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 4 publications found

Genes affected

LINC02315 (HGNC:53234): (long intergenic non-protein coding RNA 2315)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02315	NR_109758.1	n.346+79867A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02315	ENST00000651006.2	n.642+79867A>G		intron_variant	Intron 3 of 3
LINC02315	ENST00000719278.1	n.386+79867A>G		intron_variant	Intron 4 of 4
LINC02315	ENST00000719279.1	n.449+79867A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88541 AN: 151594 Hom.: 28292 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.584 AC: 88531 AN: 151712 Hom.: 28275 Cov.: 31 AF XY: 0.583 AC XY: 43198 AN XY: 74120

African (AFR) AF: 0.303 AC: 12560 AN: 41426

American (AMR) AF: 0.639 AC: 9727 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2322 AN: 3462

East Asian (EAS) AF: 0.758 AC: 3907 AN: 5152

South Asian (SAS) AF: 0.784 AC: 3785 AN: 4826

European-Finnish (FIN) AF: 0.593 AC: 6257 AN: 10556

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47724 AN: 67742

Other (OTH) AF: 0.623 AC: 1314 AN: 2110

Alfa AF: 0.671 Hom.: 105067

Bravo AF: 0.573

Asia WGS AF: 0.714 AC: 2483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1959947; hg19: chr14-41523462;