2-22421964-A-G

Variant names:

• chr2-22421964-A-G
• rs1509384
• ENST00000419013.1:n.119-6908A>G

Variant summary

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

The ENST00000419013.1(LINC03116):​n.119-6908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,038 control chromosomes in the GnomAD database, including 42,265 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 0.73 (42265 hom., cov: 32)
• Consequence: LINC03116 ENST00000419013.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 5 publications found

Genes affected

LINC03116 (HGNC:56881):

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419013.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03116	ENST00000419013.1	TSL:4	n.119-6908A>G		intron	N/A
	LINC01830	ENST00000450551.1	TSL:5	n.70+109072T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111568 AN: 151920 Hom.: 42222 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.734 AC: 111653 AN: 152038 Hom.: 42265 Cov.: 32 AF XY: 0.726 AC XY: 53908 AN XY: 74298

African (AFR) AF: 0.912 AC: 37854 AN: 41516

American (AMR) AF: 0.671 AC: 10230 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2619 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2026 AN: 5156

South Asian (SAS) AF: 0.518 AC: 2497 AN: 4820

European-Finnish (FIN) AF: 0.673 AC: 7097 AN: 10552

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47097 AN: 67956

Other (OTH) AF: 0.696 AC: 1472 AN: 2114

Alfa AF: 0.717 Hom.: 7692

Bravo AF: 0.743

Asia WGS AF: 0.501 AC: 1744 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1509384; hg19: chr2-22644836;