22-28765019-C-T

Variant names:

• chr22-28765019-C-T
• rs4820792
• ENST00000729538.1:n.306+4224C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000729538.1(ENSG00000295361):​n.306+4224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,772 control chromosomes in the GnomAD database, including 3,809 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 (3809 hom., cov: 30)
• Consequence: ENSG00000295361 ENST00000729538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 7 publications found

Genes affected

ENSG00000295361 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729538.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295361	ENST00000729538.1		n.306+4224C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32600 AN: 151654 Hom.: 3807 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.215 AC: 32645 AN: 151772 Hom.: 3809 Cov.: 30 AF XY: 0.218 AC XY: 16139 AN XY: 74162

African (AFR) AF: 0.257 AC: 10629 AN: 41376

American (AMR) AF: 0.277 AC: 4222 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2025 AN: 5098

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4810

European-Finnish (FIN) AF: 0.178 AC: 1880 AN: 10550

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10794 AN: 67918

Other (OTH) AF: 0.235 AC: 497 AN: 2114

Alfa AF: 0.175 Hom.: 725

Bravo AF: 0.229

Asia WGS AF: 0.338 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4820792; hg19: chr22-29161007;