rs1605834

Variant names:

• chr2-22353228-A-G
• rs1605834
• ENST00000450551.1:n.71-142234T>C

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.71-142234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,482 control chromosomes in the GnomAD database, including 6,733 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 0.25 (6733 hom., cov: 29)
• Consequence: ENSG00000228999 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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.71-142234T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38428 AN: 151368 Hom.: 6710 Cov.: 29

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.254 AC: 38505 AN: 151482 Hom.: 6733 Cov.: 29 AF XY: 0.251 AC XY: 18610 AN XY: 74008

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.249

Alfa AF: 0.168 Hom.: 5255

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.95
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605834; hg19: chr2-22576100;