22-34463801-A-G

Variant names:

• chr22-34463801-A-G
• rs130575

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 0.149 in 152,116 control chromosomes in the GnomAD database, including 1,798 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 0.15 (1798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 10 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22660 AN: 151998 Hom.: 1797 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.149 AC: 22672 AN: 152116 Hom.: 1798 Cov.: 32 AF XY: 0.146 AC XY: 10895 AN XY: 74376

African (AFR) AF: 0.192 AC: 7982 AN: 41510

American (AMR) AF: 0.130 AC: 1985 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3468

East Asian (EAS) AF: 0.111 AC: 571 AN: 5156

South Asian (SAS) AF: 0.0915 AC: 440 AN: 4808

European-Finnish (FIN) AF: 0.106 AC: 1128 AN: 10598

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9354 AN: 67996

Other (OTH) AF: 0.157 AC: 330 AN: 2108

Alfa AF: 0.145 Hom.: 5640

Bravo AF: 0.155

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.80
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs130575; hg19: chr22-34859793;