14-22446824-G-T

Variant names:

• chr14-22446824-G-T
• rs12147516

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 0.133 in 150,182 control chromosomes in the GnomAD database, including 1,796 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 0.13 (1796 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	NR_148361.1		n.225+34417C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.225+34417C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20053 AN: 150064 Hom.: 1801 Cov.: 25

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.133 AC: 20040 AN: 150182 Hom.: 1796 Cov.: 25 AF XY: 0.139 AC XY: 10219 AN XY: 73320

African (AFR) AF: 0.0835 AC: 3396 AN: 40664

American (AMR) AF: 0.145 AC: 2160 AN: 14890

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3460

East Asian (EAS) AF: 0.464 AC: 2371 AN: 5112

South Asian (SAS) AF: 0.250 AC: 1190 AN: 4754

European-Finnish (FIN) AF: 0.162 AC: 1673 AN: 10332

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8257 AN: 67680

Other (OTH) AF: 0.118 AC: 248 AN: 2094

Alfa AF: 0.127 Hom.: 4264

Bravo AF: 0.126

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs12147516; hg19: chr14-22915816;