12-92978962-A-G

Variant names:

• chr12-92978962-A-G
• rs7302601
• ENST00000755877.1:n.105-11725A>G

Variant summary

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

The ENST00000755877.1(LINC02413):​n.105-11725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 150,552 control chromosomes in the GnomAD database, including 47,952 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 0.79 (47952 hom., cov: 24)
• Consequence: LINC02413 ENST00000755877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 1 publications found

Genes affected

LINC02413 (HGNC:53342): (long intergenic non-protein coding RNA 2413)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 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
LINC02413	ENST00000755877.1	n.105-11725A>G		intron_variant	Intron 1 of 2
LINC02413	ENST00000755878.1	n.199-11725A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.792 AC: 119103 AN: 150434 Hom.: 47882 Cov.: 24

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.792 AC: 119228 AN: 150552 Hom.: 47952 Cov.: 24 AF XY: 0.792 AC XY: 58172 AN XY: 73426

African (AFR) AF: 0.946 AC: 38635 AN: 40860

American (AMR) AF: 0.772 AC: 11644 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2286 AN: 3466

East Asian (EAS) AF: 0.739 AC: 3726 AN: 5044

South Asian (SAS) AF: 0.774 AC: 3660 AN: 4728

European-Finnish (FIN) AF: 0.758 AC: 7836 AN: 10344

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49062 AN: 67738

Other (OTH) AF: 0.753 AC: 1570 AN: 2084

Alfa AF: 0.738 Hom.: 24316

Bravo AF: 0.798

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7302601; hg19: chr12-93372738;