22-49024350-C-T

Variant names:

• chr22-49024350-C-T
• rs4528878

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 0.0824 in 152,300 control chromosomes in the GnomAD database, including 1,316 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 0.082 (1316 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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: 0.0822 AC: 12506 AN: 152182 Hom.: 1311 Cov.: 34

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0824 AC: 12542 AN: 152300 Hom.: 1316 Cov.: 34 AF XY: 0.0797 AC XY: 5933 AN XY: 74472

African (AFR) AF: 0.246 AC: 10203 AN: 41536

American (AMR) AF: 0.0498 AC: 763 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3468

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5176

South Asian (SAS) AF: 0.00601 AC: 29 AN: 4826

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10632

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0150 AC: 1021 AN: 68034

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0173 Hom.: 16

Bravo AF: 0.0931

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4528878; hg19: chr22-49420162;