rs3811222

Variant names:

• chr14-22482025-G-A
• rs3811222

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 0.122 in 151,330 control chromosomes in the GnomAD database, including 1,593 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 0.12 (1593 hom., cov: 27)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22482025G>A		intragenic_variant
TRD-AS1	NR_148361.1	n.108-667C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000514473.2	n.108-667C>T		intron_variant	Intron 1 of 2	2
TRD-AS1	ENST00000556777.2	n.445-667C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18512 AN: 151212 Hom.: 1593 Cov.: 27

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18514 AN: 151330 Hom.: 1593 Cov.: 27 AF XY: 0.128 AC XY: 9448 AN XY: 73934

African (AFR) AF: 0.0834 AC: 3431 AN: 41158

American (AMR) AF: 0.0801 AC: 1212 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2505 AN: 5148

South Asian (SAS) AF: 0.225 AC: 1079 AN: 4796

European-Finnish (FIN) AF: 0.171 AC: 1790 AN: 10438

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7699 AN: 67876

Other (OTH) AF: 0.103 AC: 217 AN: 2098

Alfa AF: 0.118 Hom.: 1235

Bravo AF: 0.113

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.028
DANN	Benign	0.46
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3811222; hg19: chr14-22951014; COSMIC: COSV66607189;