14-22391078-T-G

Variant names:

• chr14-22391078-T-G
• rs3811244

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 0.34 in 150,016 control chromosomes in the GnomAD database, including 9,060 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 0.34 (9060 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 6 publications found

Genes affected

TRA (HGNC:12027):

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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.226-8673A>C		intron	N/A
	TRD-AS1	NR_148362.1		n.290-8673A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000514473.2	TSL:2	n.226-8673A>C		intron	N/A
	TRD-AS1	ENST00000541008.6	TSL:4	n.277-8673A>C		intron	N/A
	TRD-AS1	ENST00000545670.5	TSL:4	n.276-8673A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 50918 AN: 149896 Hom.: 9052 Cov.: 25

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.340 AC: 50939 AN: 150016 Hom.: 9060 Cov.: 25 AF XY: 0.330 AC XY: 24160 AN XY: 73216

African (AFR) AF: 0.379 AC: 15380 AN: 40570

American (AMR) AF: 0.238 AC: 3538 AN: 14896

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1005 AN: 3450

East Asian (EAS) AF: 0.0884 AC: 455 AN: 5146

South Asian (SAS) AF: 0.180 AC: 847 AN: 4702

European-Finnish (FIN) AF: 0.299 AC: 3085 AN: 10312

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25476 AN: 67646

Other (OTH) AF: 0.323 AC: 677 AN: 2098

Alfa AF: 0.356 Hom.: 41378

Bravo AF: 0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs3811244; hg19: chr14-22859482;