22-24009046-G-A

Variant names:

• chr22-24009046-G-A
• rs738809
• ENST00000757608.1:n.*179G>A

Variant summary

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

The ENST00000757608.1(ENSG00000298726):​n.*179G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,018 control chromosomes in the GnomAD database, including 39,662 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 0.72 (39662 hom., cov: 30)
• Consequence: ENSG00000298726 ENST00000757608.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 24 publications found

Genes affected

ENSG00000298726 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372959	XR_001755457.1	n.*179G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298726	ENST00000757608.1	n.*179G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109421 AN: 151902 Hom.: 39627 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.720 AC: 109501 AN: 152018 Hom.: 39662 Cov.: 30 AF XY: 0.725 AC XY: 53864 AN XY: 74296

African (AFR) AF: 0.698 AC: 28900 AN: 41424

American (AMR) AF: 0.777 AC: 11881 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2322 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3186 AN: 5168

South Asian (SAS) AF: 0.764 AC: 3679 AN: 4814

European-Finnish (FIN) AF: 0.779 AC: 8226 AN: 10562

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48890 AN: 67978

Other (OTH) AF: 0.713 AC: 1502 AN: 2108

Alfa AF: 0.720 Hom.: 54651

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs738809; hg19: chr22-24405492;