22-39089207-C-T

Variant names:

• chr22-39089207-C-T
• rs5995668

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.202 AC: 8376 AN: 41494

American (AMR) AF: 0.106 AC: 1628 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.106 AC: 551 AN: 5184

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4830

European-Finnish (FIN) AF: 0.0926 AC: 981 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6745 AN: 67990

Other (OTH) AF: 0.130 AC: 275 AN: 2110

Alfa AF: 0.110 Hom.: 172

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5995668; hg19: chr22-39485212;