rs134049

Variant names:

• chr22-27662853-C-T
• rs134049

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 0.0634 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.145 AC: 6032 AN: 41554

American (AMR) AF: 0.0290 AC: 443 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.00426 AC: 22 AN: 5160

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4826

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10626

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0365 AC: 2479 AN: 68008

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0549 Hom.: 46

Bravo AF: 0.0676

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs134049; hg19: chr22-28058812;