rs718433

Variant names:

• chr14-21767650-A-G
• rs718433

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 0.347 in 151,862 control chromosomes in the GnomAD database, including 9,389 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 0.35 (9389 hom., cov: 30)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• 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 (Cadd=9.915).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.21767650A>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52673 AN: 151742 Hom.: 9384 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.347 AC: 52690 AN: 151862 Hom.: 9389 Cov.: 30 AF XY: 0.343 AC XY: 25425 AN XY: 74214

African (AFR) AF: 0.313 AC: 12964 AN: 41432

American (AMR) AF: 0.287 AC: 4376 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5158

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4812

European-Finnish (FIN) AF: 0.358 AC: 3774 AN: 10540

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26667 AN: 67892

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.361 Hom.: 8809

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	9.9
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs718433; hg19: -;