9-22956520-T-C

Position:

• chr9-22956520-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.925 in 152,256 control chromosomes in the GnomAD database, including 65,204 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 0.92 (65204 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22956520T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284418	ENST00000640003.1	n.368+49560A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140755 AN: 152138 Hom.: 65184 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.925 AC: 140828 AN: 152256 Hom.: 65204 Cov.: 32 AF XY: 0.925 AC XY: 68877 AN XY: 74438

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.917

Alfa AF: 0.928 Hom.: 62554

Bravo AF: 0.921

Asia WGS AF: 0.905 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1599698; hg19: chr9-22956519;