rs10498603

Variant names:

• chr14-86144612-C-G
• rs10498603
• ENST00000655493.1:n.391-16252C>G

Your query was ambiguous. Multiple possible variants found:

• chr14-86144612-C-G
• chr14-86144612-C-T

Variant summary

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

The ENST00000655493.1(LINC02328):​n.391-16252C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,228 control chromosomes in the GnomAD database, including 123 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 (123 hom., cov: 31)
• Consequence: LINC02328 ENST00000655493.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655493.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	ENST00000655493.1		n.391-16252C>G		intron	N/A
	LINC02328	ENST00000668344.4		n.568-16252C>G		intron	N/A
	LINC02328	ENST00000752522.1		n.433-16252C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3244 AN: 152110 Hom.: 122 Cov.: 31

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0214 AC: 3260 AN: 152228 Hom.: 123 Cov.: 31 AF XY: 0.0243 AC XY: 1809 AN XY: 74426

African (AFR) AF: 0.00395 AC: 164 AN: 41554

American (AMR) AF: 0.0753 AC: 1151 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3464

East Asian (EAS) AF: 0.118 AC: 612 AN: 5180

South Asian (SAS) AF: 0.0412 AC: 198 AN: 4804

European-Finnish (FIN) AF: 0.0353 AC: 374 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0104 AC: 709 AN: 68012

Other (OTH) AF: 0.0198 AC: 42 AN: 2116

Alfa AF: 0.00400 Hom.: 0

Bravo AF: 0.0247

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-0.083

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10498603;

hg19: chr14-86610956;