ENST00000433835.3:c.432-2025A>G

Variant names:

• chr22-23892747-A-G
• rs12485068
• ENST00000433835.3:c.432-2025A>G

Variant summary

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

The ENST00000433835.3(ENSG00000251357):​c.432-2025A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,018 control chromosomes in the GnomAD database, including 3,126 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 0.20 (3126 hom., cov: 32)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 4 publications found

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433835.3. 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
	ENSG00000251357	ENST00000433835.3	TSL:5	c.432-2025A>G		intron	N/A	ENSP00000400325.3
	ENSG00000290199	ENST00000717616.1		n.213-1281T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30028 AN: 151896 Hom.: 3116 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.198 AC: 30069 AN: 152018 Hom.: 3126 Cov.: 32 AF XY: 0.203 AC XY: 15048 AN XY: 74310

African (AFR) AF: 0.224 AC: 9288 AN: 41452

American (AMR) AF: 0.236 AC: 3597 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 456 AN: 3466

East Asian (EAS) AF: 0.186 AC: 961 AN: 5170

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4822

European-Finnish (FIN) AF: 0.227 AC: 2404 AN: 10574

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11638 AN: 67956

Other (OTH) AF: 0.178 AC: 376 AN: 2108

Alfa AF: 0.195 Hom.: 413

Bravo AF: 0.197

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.40
PhyloP100		0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12485068; hg19: chr22-24234934;