22-28802163-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000226471	ENST00000418292.1	n.34+1426T>G		intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000451486.5	n.103+169T>G		intron_variant	Intron 1 of 1	5
ENSG00000226471	ENST00000458080.1	n.55+1426T>G		intron_variant	Intron 1 of 3	3

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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.375

Alfa AF: 0.343 Hom.: 4472

Bravo AF: 0.398

Asia WGS AF: 0.612 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3788409; hg19: chr22-29198151;