chr14-22436073-T-C

Variant names:

• chr14-22436073-T-C
• rs8021297

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 0.455 in 150,120 control chromosomes in the GnomAD database, including 16,124 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 0.45 (16124 hom., cov: 24)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 5 publications found

Genes affected

TRA (HGNC:12027):

TRD (HGNC:12252):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514473.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	NR_148361.1		n.225+45168A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.225+45168A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68190 AN: 150002 Hom.: 16117 Cov.: 24

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.455 AC: 68240 AN: 150120 Hom.: 16124 Cov.: 24 AF XY: 0.460 AC XY: 33656 AN XY: 73194

African (AFR) AF: 0.351 AC: 14268 AN: 40650

American (AMR) AF: 0.374 AC: 5586 AN: 14922

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1917 AN: 3458

East Asian (EAS) AF: 0.698 AC: 3596 AN: 5152

South Asian (SAS) AF: 0.666 AC: 3165 AN: 4752

European-Finnish (FIN) AF: 0.493 AC: 5082 AN: 10306

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33024 AN: 67602

Other (OTH) AF: 0.432 AC: 899 AN: 2080

Alfa AF: 0.488 Hom.: 11614

Bravo AF: 0.435

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.49
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs8021297; hg19: chr14-22905065;