chr14-22546932-T-C

Variant names:

• chr14-22546932-T-C
• rs943888

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 0.844 in 152,224 control chromosomes in the GnomAD database, including 54,775 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 0.84 (54775 hom., cov: 32)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 3 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=0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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: 0.844 AC: 128347 AN: 152106 Hom.: 54711 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.844 AC: 128471 AN: 152224 Hom.: 54775 Cov.: 32 AF XY: 0.838 AC XY: 62365 AN XY: 74408

African (AFR) AF: 0.939 AC: 39008 AN: 41544

American (AMR) AF: 0.809 AC: 12364 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2897 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2604 AN: 5178

South Asian (SAS) AF: 0.770 AC: 3714 AN: 4822

European-Finnish (FIN) AF: 0.795 AC: 8433 AN: 10602

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56584 AN: 68002

Other (OTH) AF: 0.863 AC: 1824 AN: 2114

Alfa AF: 0.833 Hom.: 136766

Bravo AF: 0.848

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.88
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs943888;