rs1882704

Variant names:

• chr14-22456360-G-A
• rs1882704

Your query was ambiguous. Multiple possible variants found:

• chr14-22456360-G-A
• chr14-22456360-G-C

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 0.764 in 150,458 control chromosomes in the GnomAD database, including 44,124 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 0.76 (44124 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22456360G>A		intragenic_variant
TRD		n.22456360G>A		intragenic_variant
TRD-AS1	NR_148361.1	n.225+24881C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.225+24881C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 114858 AN: 150340 Hom.: 44078 Cov.: 25

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.764 AC: 114966 AN: 150458 Hom.: 44124 Cov.: 25 AF XY: 0.765 AC XY: 56211 AN XY: 73440

African (AFR) AF: 0.849 AC: 34653 AN: 40814

American (AMR) AF: 0.716 AC: 10703 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2552 AN: 3454

East Asian (EAS) AF: 0.839 AC: 4340 AN: 5172

South Asian (SAS) AF: 0.805 AC: 3827 AN: 4756

European-Finnish (FIN) AF: 0.717 AC: 7403 AN: 10320

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49084 AN: 67716

Other (OTH) AF: 0.744 AC: 1548 AN: 2082

Alfa AF: 0.737 Hom.: 176710

Bravo AF: 0.767

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.69
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1882704; hg19: chr14-22925352;