rs2303970

Variant names:

• chr12-74077560-C-T
• rs2303970
• ENST00000653134.1:n.777+73442G>A

Variant summary

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

The ENST00000653134.1(LINC02882):​n.777+73442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,982 control chromosomes in the GnomAD database, including 24,792 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 0.55 (24792 hom., cov: 32)
• Consequence: LINC02882 ENST00000653134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02882	ENST00000653134.1	n.777+73442G>A		intron_variant	Intron 8 of 8
LINC02882	ENST00000663261.1	n.709+73442G>A		intron_variant	Intron 8 of 11
LINC02882	ENST00000665907.1	n.636+73442G>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83801 AN: 151864 Hom.: 24743 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.552 AC: 83905 AN: 151982 Hom.: 24792 Cov.: 32 AF XY: 0.547 AC XY: 40648 AN XY: 74280

African (AFR) AF: 0.768 AC: 31859 AN: 41486

American (AMR) AF: 0.553 AC: 8424 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1666 AN: 3464

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5174

South Asian (SAS) AF: 0.502 AC: 2416 AN: 4816

European-Finnish (FIN) AF: 0.420 AC: 4431 AN: 10542

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31910 AN: 67946

Other (OTH) AF: 0.499 AC: 1053 AN: 2110

Alfa AF: 0.498 Hom.: 61464

Bravo AF: 0.573

Asia WGS AF: 0.441 AC: 1531 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.61
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2303970; hg19: chr12-74471340;