chr12-74150244-A-C

Variant names:

• chr12-74150244-A-C
• rs10506702
• ENST00000549905.5:n.697+758T>G

Variant summary

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

The ENST00000549905.5(LINC02882):​n.697+758T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 152,250 control chromosomes in the GnomAD database, including 482 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 0.061 (482 hom., cov: 32)
• Consequence: LINC02882 ENST00000549905.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 2 publications found

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549905.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02882	NR_038300.1		n.697+758T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02882	ENST00000549905.5	TSL:1	n.697+758T>G		intron	N/A
	LINC02882	ENST00000662107.2		n.798T>G		non_coding_transcript_exon	Exon 6 of 6
	LINC02882	ENST00000716244.1		n.576T>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9280 AN: 152132 Hom.: 466 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0612 AC: 9316 AN: 152250 Hom.: 482 Cov.: 32 AF XY: 0.0623 AC XY: 4637 AN XY: 74446

African (AFR) AF: 0.0541 AC: 2246 AN: 41548

American (AMR) AF: 0.168 AC: 2570 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3472

East Asian (EAS) AF: 0.126 AC: 653 AN: 5176

South Asian (SAS) AF: 0.0784 AC: 379 AN: 4832

European-Finnish (FIN) AF: 0.0382 AC: 405 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2826 AN: 68016

Other (OTH) AF: 0.0614 AC: 130 AN: 2116

Alfa AF: 0.0455 Hom.: 80

Bravo AF: 0.0722

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.42
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10506702; hg19: chr12-74544024;