22-28802163-T-G

Variant names:

• chr22-28802163-T-G
• rs3788409
• ENST00000418292.1:n.34+1426T>G

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.34+1426T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,902 control chromosomes in the GnomAD database, including 13,411 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 0.40 (13411 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 13 publications found

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418292.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226471	ENST00000418292.1	TSL:3	n.34+1426T>G		intron	N/A
	ENSG00000226471	ENST00000451486.5	TSL:5	n.103+169T>G		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.55+1426T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60575 AN: 151784 Hom.: 13383 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.399 AC: 60659 AN: 151902 Hom.: 13411 Cov.: 31 AF XY: 0.403 AC XY: 29900 AN XY: 74238

African (AFR) AF: 0.557 AC: 23014 AN: 41354

American (AMR) AF: 0.296 AC: 4527 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3505 AN: 5174

South Asian (SAS) AF: 0.536 AC: 2591 AN: 4830

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10552

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20890 AN: 67940

Other (OTH) AF: 0.375 AC: 790 AN: 2104

Alfa AF: 0.343 Hom.: 5011

Bravo AF: 0.398

Asia WGS AF: 0.612 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3788409;

hg19: chr22-29198151;