chr22-23423078-A-G

Variant names:

• chr22-23423078-A-G
• rs4822410

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 0.14 in 151,944 control chromosomes in the GnomAD database, including 2,258 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 0.14 (2258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.139 AC: 21168 AN: 151826 Hom.: 2253 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.140 AC: 21198 AN: 151944 Hom.: 2258 Cov.: 32 AF XY: 0.148 AC XY: 10992 AN XY: 74274

African (AFR) AF: 0.152 AC: 6297 AN: 41434

American (AMR) AF: 0.271 AC: 4124 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2636 AN: 5152

South Asian (SAS) AF: 0.201 AC: 963 AN: 4798

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10570

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0756 AC: 5136 AN: 67964

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.0985 Hom.: 4451

Bravo AF: 0.153

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.80
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4822410; hg19: chr22-23765265;