ENST00000423504.3:n.337-2485C>T

Variant names:

• chr6-24746511-C-T
• rs12190789
• ENST00000423504.3:n.337-2485C>T

Variant summary

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

The ENST00000423504.3(LINC02828):​n.337-2485C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,890 control chromosomes in the GnomAD database, including 1,081 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 0.11 (1081 hom., cov: 32)
• Consequence: LINC02828 ENST00000423504.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 6 publications found

Genes affected

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

ENSG00000307310 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02828	NR_183315.1	n.43-2485C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02828	ENST00000423504.3	n.337-2485C>T		intron_variant	Intron 1 of 2	2
LINC02828	ENST00000453179.1	n.46-2485C>T		intron_variant	Intron 1 of 2	4
LINC02828	ENST00000665572.2	n.268-2485C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16286 AN: 151772 Hom.: 1081 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.107 AC: 16285 AN: 151890 Hom.: 1081 Cov.: 32 AF XY: 0.106 AC XY: 7902 AN XY: 74228

African (AFR) AF: 0.0327 AC: 1348 AN: 41240

American (AMR) AF: 0.117 AC: 1788 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.113 AC: 585 AN: 5186

South Asian (SAS) AF: 0.0797 AC: 385 AN: 4828

European-Finnish (FIN) AF: 0.137 AC: 1446 AN: 10580

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9930 AN: 67990

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.132 Hom.: 1018

Bravo AF: 0.105

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.60
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12190789; hg19: chr6-24746739;