rs12752888

Variant names:

• chr1-54527266-T-C
• rs12752888
• ENST00000768431.1:n.242+1266A>G

Variant summary

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

The ENST00000768431.1(LINC02784):​n.242+1266A>G variant causes a intron 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 ENST00000768431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• Publications: 6 publications found

Genes affected

LINC02784 (HGNC:54304): (long intergenic non-protein coding RNA 2784)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02784	NR_183669.1	n.246+1266A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02784	ENST00000768431.1	n.242+1266A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.262 AC: 10859 AN: 41506

American (AMR) AF: 0.230 AC: 3520 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5174

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4810

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19039 AN: 67988

Other (OTH) AF: 0.259 AC: 548 AN: 2112

Alfa AF: 0.270 Hom.: 25253

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
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs12752888; hg19: chr1-54992939;