rs12190789

Positions:

• chr6-24746511-C-T

Variant summary

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

The NR_183315.1(LINC02828):​n.43-2485C>T 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 0.107 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 NR_183315.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02828	NR_183315.1	n.43-2485C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02828	ENST00000665572.1	n.268-2485C>T		intron_variant, non_coding_transcript_variant
LINC02828	ENST00000423504.2	n.49-2485C>T		intron_variant, non_coding_transcript_variant		2
LINC02828	ENST00000453179.1	n.46-2485C>T		intron_variant, non_coding_transcript_variant		4
LINC02828	ENST00000668439.1	n.238-5052C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0327

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.128 Hom.: 498

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12190789; hg19: chr6-24746739;