chr14-22452288-G-T

Variant names:

• chr14-22452288-G-T
• rs11848747

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 0.145 in 150,950 control chromosomes in the GnomAD database, including 2,677 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 0.14 (2677 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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+28953C>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+28953C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21800 AN: 150832 Hom.: 2659 Cov.: 26

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0448

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.145 AC: 21841 AN: 150950 Hom.: 2677 Cov.: 26 AF XY: 0.142 AC XY: 10445 AN XY: 73724

African (AFR) AF: 0.339 AC: 13816 AN: 40810

American (AMR) AF: 0.102 AC: 1542 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.0448 AC: 155 AN: 3456

East Asian (EAS) AF: 0.00715 AC: 37 AN: 5174

South Asian (SAS) AF: 0.0468 AC: 224 AN: 4790

European-Finnish (FIN) AF: 0.0628 AC: 660 AN: 10504

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5048 AN: 67844

Other (OTH) AF: 0.136 AC: 285 AN: 2100

Alfa AF: 0.0814 Hom.: 993

Bravo AF: 0.157

Asia WGS AF: 0.0490 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.54
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11848747; hg19: chr14-22921280;