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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22487722G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;