22-43104206-G-T

Variant names:

• chr22-43104206-G-T
• rs5759167

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 0.405 in 152,214 control chromosomes in the GnomAD database, including 13,458 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 0.40 (13458 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 119 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61601 AN: 152096 Hom.: 13446 Cov.: 34

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.405 AC: 61646 AN: 152214 Hom.: 13458 Cov.: 34 AF XY: 0.403 AC XY: 30011 AN XY: 74424

African (AFR) AF: 0.247 AC: 10243 AN: 41544

American (AMR) AF: 0.364 AC: 5567 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3464

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2054 AN: 4826

European-Finnish (FIN) AF: 0.475 AC: 5038 AN: 10600

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33876 AN: 68004

Other (OTH) AF: 0.419 AC: 884 AN: 2108

Alfa AF: 0.471 Hom.: 77851

Bravo AF: 0.390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.58
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs5759167; hg19: chr22-43500212;