rs227869

Variant names:

• chr14-22487722-G-A
• rs227869

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 0.588 in 151,232 control chromosomes in the GnomAD database, including 26,788 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 0.59 (26788 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 7 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.588 AC: 88870 AN: 151114 Hom.: 26785 Cov.: 26

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.588 AC: 88909 AN: 151232 Hom.: 26788 Cov.: 26 AF XY: 0.584 AC XY: 43200 AN XY: 73912

African (AFR) AF: 0.691 AC: 28403 AN: 41080

American (AMR) AF: 0.422 AC: 6406 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2119 AN: 3462

East Asian (EAS) AF: 0.803 AC: 4139 AN: 5154

South Asian (SAS) AF: 0.515 AC: 2468 AN: 4794

European-Finnish (FIN) AF: 0.581 AC: 6083 AN: 10466

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37438 AN: 67790

Other (OTH) AF: 0.571 AC: 1205 AN: 2110

Alfa AF: 0.555 Hom.: 39822

Bravo AF: 0.585

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.7
DANN	Benign	0.71
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs227869; hg19: chr14-22956710;