22-27420823-G-A

Variant names:

• chr22-27420823-G-A
• rs733164
• ENST00000729519.1:n.-121C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000729519.1(ENSG00000280445):​n.-121C>T variant causes a upstream gene change. The variant allele was found at a frequency of 0.3 in 152,062 control chromosomes in the GnomAD database, including 6,974 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 0.30 (6974 hom., cov: 32)
• Consequence: ENSG00000280445 ENST00000729519.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.83
• Publications: 19 publications found

Genes affected

ENSG00000280445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280445	ENST00000729519.1		n.-121C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45592 AN: 151944 Hom.: 6973 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.300 AC: 45621 AN: 152062 Hom.: 6974 Cov.: 32 AF XY: 0.297 AC XY: 22053 AN XY: 74338

African (AFR) AF: 0.326 AC: 13517 AN: 41470

American (AMR) AF: 0.306 AC: 4676 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1257 AN: 3466

East Asian (EAS) AF: 0.137 AC: 706 AN: 5166

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4808

European-Finnish (FIN) AF: 0.305 AC: 3227 AN: 10586

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19900 AN: 67954

Other (OTH) AF: 0.296 AC: 625 AN: 2112

Alfa AF: 0.298 Hom.: 20437

Bravo AF: 0.307

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	17
DANN	Benign	0.78
PhyloP100		6.8

Splicing

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

Other links and lift over

dbSNP: rs733164; hg19: chr22-27816784; COSMIC: COSV52393903;