rs10498603

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668344.3(LINC02328):​n.526-16252C>G variant causes a intron, non coding transcript 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 ENST00000668344.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02328	ENST00000668344.3	n.526-16252C>G		intron_variant, non_coding_transcript_variant
LINC02328	ENST00000655493.1	n.391-16252C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00395

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.0353

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0198

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498603; hg19: chr14-86610956;