14-22546932-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22546932T>C		intragenic_variant

Ensembl

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

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 v4.3

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; hg19: -;