chr22-28757771-C-T

Variant names:

• chr22-28757771-C-T
• rs5752792

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 0.876 in 152,120 control chromosomes in the GnomAD database, including 58,834 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 0.88 (58834 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.876 AC: 133162 AN: 152000 Hom.: 58763 Cov.: 30

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.876 AC: 133294 AN: 152120 Hom.: 58834 Cov.: 30 AF XY: 0.881 AC XY: 65546 AN XY: 74384

African (AFR) AF: 0.968 AC: 40159 AN: 41508

American (AMR) AF: 0.874 AC: 13314 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5162 AN: 5170

South Asian (SAS) AF: 0.957 AC: 4621 AN: 4828

European-Finnish (FIN) AF: 0.866 AC: 9178 AN: 10594

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55213 AN: 67990

Other (OTH) AF: 0.867 AC: 1832 AN: 2114

Alfa AF: 0.833 Hom.: 44558

Bravo AF: 0.878

Asia WGS AF: 0.972 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs5752792; hg19: chr22-29153759;