22-26633581-A-G

Variant names:

• chr22-26633581-A-G
• rs2009066
• ENST00000840167.1:n.791-1048T>C

Variant summary

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

The ENST00000840167.1(ENSG00000309298):​n.791-1048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,852 control chromosomes in the GnomAD database, including 26,723 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 0.59 (26723 hom., cov: 30)
• Consequence: ENSG00000309298 ENST00000840167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 4 publications found

Genes affected

ENSG00000309298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840167.1. 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
	ENSG00000309298	ENST00000840167.1		n.791-1048T>C		intron	N/A
	ENSG00000309298	ENST00000840168.1		n.215-1048T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88986 AN: 151734 Hom.: 26709 Cov.: 30

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.586 AC: 89047 AN: 151852 Hom.: 26723 Cov.: 30 AF XY: 0.587 AC XY: 43580 AN XY: 74224

African (AFR) AF: 0.445 AC: 18427 AN: 41398

American (AMR) AF: 0.625 AC: 9520 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2656 AN: 5148

South Asian (SAS) AF: 0.587 AC: 2825 AN: 4810

European-Finnish (FIN) AF: 0.669 AC: 7059 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44120 AN: 67934

Other (OTH) AF: 0.609 AC: 1281 AN: 2104

Alfa AF: 0.613 Hom.: 8237

Bravo AF: 0.582

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.72
PhyloP100		1.1

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: rs2009066;

hg19: chr22-27029545;