rs2090052

chr8-22705582-G-A

Variant summary

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

The ENST00000523627.1(ENSG00000253125):n.164+15269G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,180 control chromosomes in the GnomAD database, including 3,692 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 0.22 (3692 hom., cov: 33)
• Consequence: ENST00000523627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523627.1	n.164+15269G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33330 AN: 152062 Hom.: 3684 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.219 AC: 33371 AN: 152180 Hom.: 3692 Cov.: 33 AF XY: 0.220 AC XY: 16371 AN XY: 74404

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.218

Alfa AF: 0.230 Hom.: 3019

Bravo AF: 0.219

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090052; hg19: chr8-22563095;