12-68378458-T-C

Position:

• chr12-68378458-T-C

Variant summary

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

The ENST00000693550.2(LINC02384):​n.307-44794A>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 0.9 in 152,238 control chromosomes in the GnomAD database, including 61,800 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 0.90 (61800 hom., cov: 32)
• Consequence: LINC02384 ENST00000693550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

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 = 0.953 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
LINC02384	ENST00000693550.2	n.307-44794A>G		intron_variant, non_coding_transcript_variant
LINC02384	ENST00000539404.1	n.68+25275A>G		intron_variant, non_coding_transcript_variant		3
LINC02384	ENST00000546086.1	n.154-44794A>G		intron_variant, non_coding_transcript_variant		3
LINC02384	ENST00000686524.2	n.390-44794A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136940 AN: 152120 Hom.: 61744 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.900 AC: 137057 AN: 152238 Hom.: 61800 Cov.: 32 AF XY: 0.903 AC XY: 67248 AN XY: 74436

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.921

Alfa AF: 0.883 Hom.: 9670

Bravo AF: 0.904

Asia WGS AF: 0.953 AC: 3313 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	0.014
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4913441; hg19: chr12-68772238;