rs12752888

chr1-54527266-T-C

Variant summary

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

The NR_183669.1(LINC02784):n.246+1266A>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 0.255 in 152,104 control chromosomes in the GnomAD database, including 5,233 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 0.26 (5233 hom., cov: 32)
• Consequence: LINC02784 NR_183669.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804

Genes affected

LINC02784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02784	NR_183669.1	n.246+1266A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38788 AN: 151986 Hom.: 5224 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0307

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.255 AC: 38824 AN: 152104 Hom.: 5233 Cov.: 32 AF XY: 0.250 AC XY: 18601 AN XY: 74340

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.259

Alfa AF: 0.273 Hom.: 11966

Bravo AF: 0.255

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.9
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12752888; hg19: chr1-54992939;