14-22288387-T-C

Variant names:

• chr14-22288387-T-C
• rs10129606

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 0.371 in 148,588 control chromosomes in the GnomAD database, including 10,593 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 0.37 (10593 hom., cov: 23)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 4 publications found

Genes affected

TRA (HGNC:12027):

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

LOC107984649 (HGNC:):

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 = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.271-87005A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55127 AN: 148470 Hom.: 10576 Cov.: 23

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.371 AC: 55196 AN: 148588 Hom.: 10593 Cov.: 23 AF XY: 0.366 AC XY: 26464 AN XY: 72404

African (AFR) AF: 0.457 AC: 18347 AN: 40138

American (AMR) AF: 0.334 AC: 4879 AN: 14620

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1116 AN: 3444

East Asian (EAS) AF: 0.171 AC: 871 AN: 5108

South Asian (SAS) AF: 0.371 AC: 1738 AN: 4680

European-Finnish (FIN) AF: 0.318 AC: 3196 AN: 10042

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 23988 AN: 67296

Other (OTH) AF: 0.373 AC: 769 AN: 2062

Alfa AF: 0.357 Hom.: 40072

Bravo AF: 0.375

Asia WGS AF: 0.272 AC: 944 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs10129606; hg19: chr14-22756270;