rs134049

Positions:

• chr22-27662853-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;