14-22434939-G-T

Variant names:

• chr14-22434939-G-T
• rs3811232

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 0.28 in 150,350 control chromosomes in the GnomAD database, including 6,762 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 0.28 (6762 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22434939G>T		intragenic_variant
TRD		n.22434939G>T		intragenic_variant
TRD-AS1	NR_148361.1	n.225+46302C>A		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+46302C>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42098 AN: 150232 Hom.: 6758 Cov.: 25

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.280 AC: 42122 AN: 150350 Hom.: 6762 Cov.: 25 AF XY: 0.280 AC XY: 20515 AN XY: 73386

African (AFR) AF: 0.131 AC: 5360 AN: 40852

American (AMR) AF: 0.210 AC: 3142 AN: 14928

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1346 AN: 3464

East Asian (EAS) AF: 0.186 AC: 955 AN: 5142

South Asian (SAS) AF: 0.367 AC: 1741 AN: 4750

European-Finnish (FIN) AF: 0.352 AC: 3635 AN: 10340

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24879 AN: 67590

Other (OTH) AF: 0.281 AC: 589 AN: 2094

Alfa AF: 0.334 Hom.: 15070

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3811232; hg19: chr14-22903931;