2-22328233-A-C

Variant names:

• chr2-22328233-A-C
• rs12992463
• ENST00000450551.1:n.71-117239T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450551.1(ENSG00000228999):​n.71-117239T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,102 control chromosomes in the GnomAD database, including 11,767 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 0.37 (11767 hom., cov: 32)
• Consequence: ENSG00000228999 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

Genes affected

ENSG00000228999 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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
ENSG00000228999	ENST00000450551.1	n.71-117239T>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56243 AN: 151984 Hom.: 11771 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.370 AC: 56238 AN: 152102 Hom.: 11767 Cov.: 32 AF XY: 0.363 AC XY: 27010 AN XY: 74344

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.361

Alfa AF: 0.463 Hom.: 33087

Bravo AF: 0.355

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12992463; hg19: chr2-22551105;