rs4493363

Variant names:

• chr22-34748420-G-A
• rs4493363

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 0.246 in 152,032 control chromosomes in the GnomAD database, including 5,715 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 0.25 (5715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 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: 0.246 AC: 37332 AN: 151914 Hom.: 5705 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.246 AC: 37355 AN: 152032 Hom.: 5715 Cov.: 32 AF XY: 0.254 AC XY: 18895 AN XY: 74312

African (AFR) AF: 0.0685 AC: 2844 AN: 41490

American (AMR) AF: 0.330 AC: 5028 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1351 AN: 5178

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4309 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20158 AN: 67946

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.269 Hom.: 747

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4493363; hg19: chr22-35144411;