chr22-23923472-C-T

Variant names:

• chr22-23923472-C-T
• rs4822458
• ENST00000703580.1:n.386+2972G>A

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.386+2972G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,010 control chromosomes in the GnomAD database, including 16,584 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 0.43 (16584 hom., cov: 32)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 37 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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
ENSG00000290199	ENST00000703580.1	n.386+2972G>A		intron_variant	Intron 3 of 3
ENSG00000290199	ENST00000717616.1	n.212+2972G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65253 AN: 151894 Hom.: 16572 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.429 AC: 65266 AN: 152010 Hom.: 16584 Cov.: 32 AF XY: 0.439 AC XY: 32616 AN XY: 74298

African (AFR) AF: 0.142 AC: 5878 AN: 41452

American (AMR) AF: 0.494 AC: 7545 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2352 AN: 5162

South Asian (SAS) AF: 0.587 AC: 2823 AN: 4812

European-Finnish (FIN) AF: 0.609 AC: 6439 AN: 10568

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.545 AC: 37034 AN: 67976

Other (OTH) AF: 0.436 AC: 918 AN: 2106

Alfa AF: 0.511 Hom.: 22490

Bravo AF: 0.406

Asia WGS AF: 0.513 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4822458; hg19: chr22-24265659;