14-22139542-G-T

Variant names:

• chr14-22139542-G-T
• rs1474476

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 0.103 in 151,312 control chromosomes in the GnomAD database, including 888 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 0.10 (888 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15630 AN: 151194 Hom.: 887 Cov.: 27

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.103 AC: 15642 AN: 151312 Hom.: 888 Cov.: 27 AF XY: 0.102 AC XY: 7513 AN XY: 73910

African (AFR) AF: 0.144 AC: 5935 AN: 41112

American (AMR) AF: 0.102 AC: 1539 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.115 AC: 594 AN: 5158

South Asian (SAS) AF: 0.0926 AC: 444 AN: 4796

European-Finnish (FIN) AF: 0.0529 AC: 556 AN: 10506

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5753 AN: 67846

Other (OTH) AF: 0.0962 AC: 202 AN: 2100

Alfa AF: 0.0934 Hom.: 2603

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.050
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs1474476; hg19: chr14-22607502;