22-39089207-C-T

Position:

• chr22-39089207-C-T

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 0.126 in 152,174 control chromosomes in the GnomAD database, including 1,430 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 0.13 (1430 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39089207C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19210 AN: 152056 Hom.: 1423 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0705

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.126 AC: 19238 AN: 152174 Hom.: 1430 Cov.: 33 AF XY: 0.122 AC XY: 9104 AN XY: 74402

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.130

Alfa AF: 0.107 Hom.: 159

Bravo AF: 0.133

Asia WGS AF: 0.0770 AC: 268 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	2.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5995668; hg19: chr22-39485212;