chr22-27662853-C-T

Variant names:

• chr22-27662853-C-T
• rs134049

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0634 in 152,264 control chromosomes in the GnomAD database, including 512 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 0.063 (512 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0633 AC: 9631 AN: 152146 Hom.: 512 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0634 AC: 9649 AN: 152264 Hom.: 512 Cov.: 33 AF XY: 0.0604 AC XY: 4501 AN XY: 74468

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0290

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.00426

Gnomad4 SAS AF: 0.0371

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0521 Hom.: 41

Bravo AF: 0.0676

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs134049; hg19: chr22-28058812;