22-28829512-G-A

Variant names:

• chr22-28829512-G-A
• rs5752809
• ENST00000418292.1:n.35-9348G>A

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.35-9348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,764 control chromosomes in the GnomAD database, including 13,304 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 (13304 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 11 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226471	ENST00000418292.1	TSL:3	n.35-9348G>A		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.263+7333G>A		intron	N/A
	ENSG00000226471	ENST00000687270.2		n.268+7333G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60355 AN: 151648 Hom.: 13279 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.398 AC: 60435 AN: 151764 Hom.: 13304 Cov.: 31 AF XY: 0.401 AC XY: 29757 AN XY: 74142

African (AFR) AF: 0.557 AC: 23025 AN: 41368

American (AMR) AF: 0.298 AC: 4533 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1145 AN: 3464

East Asian (EAS) AF: 0.675 AC: 3467 AN: 5134

South Asian (SAS) AF: 0.536 AC: 2579 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3796 AN: 10504

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20829 AN: 67952

Other (OTH) AF: 0.377 AC: 794 AN: 2106

Alfa AF: 0.372 Hom.: 1486

Bravo AF: 0.398

Asia WGS AF: 0.609 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs5752809; hg19: chr22-29225500;