chr2-22275718-G-A

Variant names:

• chr2-22275718-G-A
• rs12151565
• ENST00000450551.1:n.71-64724C>T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.71-64724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,178 control chromosomes in the GnomAD database, including 606 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 0.068 (606 hom., cov: 31)
• Consequence: ENSG00000228999 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 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.71-64724C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10317 AN: 152060 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0679 AC: 10336 AN: 152178 Hom.: 606 Cov.: 31 AF XY: 0.0683 AC XY: 5085 AN XY: 74420

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0604 Hom.: 84

Bravo AF: 0.0778

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12151565; hg19: chr2-22498590;