chr15-98332800-G-C

Variant names:

• chr15-98332800-G-C
• rs970843
• ENST00000661847.1:n.438-5347C>G

Variant summary

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

The NR_146567.1(LINC02351):​n.191-5347C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,158 control chromosomes in the GnomAD database, including 2,811 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 0.19 (2811 hom., cov: 33)
• Consequence: LINC02351 NR_146567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 8 publications found

Genes affected

LINC02351 (HGNC:53273): (long intergenic non-protein coding RNA 2351)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02351	NR_146567.1	n.191-5347C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02351	ENST00000661847.1	n.438-5347C>G		intron_variant	Intron 2 of 3
LINC02351	ENST00000717131.1	n.682-8384C>G		intron_variant	Intron 3 of 4
LINC02351	ENST00000717132.1	n.279-5347C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28280 AN: 152042 Hom.: 2810 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.186 AC: 28300 AN: 152158 Hom.: 2811 Cov.: 33 AF XY: 0.184 AC XY: 13696 AN XY: 74376

African (AFR) AF: 0.192 AC: 7979 AN: 41530

American (AMR) AF: 0.120 AC: 1832 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.0793 AC: 410 AN: 5170

South Asian (SAS) AF: 0.159 AC: 769 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2573 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13667 AN: 67978

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.190 Hom.: 1570

Bravo AF: 0.178

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs970843; hg19: chr15-98876029;