rs10498598

Variant names:

• chr14-85966239-A-G
• rs10498598
• ENST00000557195.5:n.152+31378A>G

Variant summary

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

The ENST00000557195.5(LINC02328):​n.152+31378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 151,772 control chromosomes in the GnomAD database, including 131 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 0.021 (131 hom., cov: 30)
• Consequence: LINC02328 ENST00000557195.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 1 publications found

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02328	NR_110155.1	n.184+31378A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02328	ENST00000557195.5	n.152+31378A>G		intron_variant	Intron 1 of 4	3
LINC02328	ENST00000654590.3	n.289+31378A>G		intron_variant	Intron 1 of 3
LINC02328	ENST00000654941.1	n.236+31378A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3195 AN: 151654 Hom.: 130 Cov.: 30

Gnomad AFR AF: 0.00398

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00992

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0212 AC: 3211 AN: 151772 Hom.: 131 Cov.: 30 AF XY: 0.0239 AC XY: 1771 AN XY: 74180

African (AFR) AF: 0.00397 AC: 165 AN: 41530

American (AMR) AF: 0.0706 AC: 1074 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3468

East Asian (EAS) AF: 0.132 AC: 681 AN: 5156

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4824

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00992 AC: 671 AN: 67654

Other (OTH) AF: 0.0214 AC: 45 AN: 2106

Alfa AF: 0.0235 Hom.: 20

Bravo AF: 0.0246

Asia WGS AF: 0.0880 AC: 302 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10498598; hg19: chr14-86432583;