14-22436733-A-G

Variant names:

• chr14-22436733-A-G
• rs11623995

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 0.737 in 150,058 control chromosomes in the GnomAD database, including 41,896 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 0.74 (41896 hom., cov: 24)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 2 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22436733A>G		intragenic_variant
TRD		n.22436733A>G		intragenic_variant
TRD-AS1	NR_148361.1	n.225+44508T>C		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+44508T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.737 AC: 110506 AN: 149940 Hom.: 41841 Cov.: 24

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.737 AC: 110622 AN: 150058 Hom.: 41896 Cov.: 24 AF XY: 0.739 AC XY: 54096 AN XY: 73186

African (AFR) AF: 0.924 AC: 37598 AN: 40682

American (AMR) AF: 0.665 AC: 9846 AN: 14806

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2297 AN: 3456

East Asian (EAS) AF: 0.877 AC: 4504 AN: 5134

South Asian (SAS) AF: 0.782 AC: 3700 AN: 4730

European-Finnish (FIN) AF: 0.657 AC: 6779 AN: 10324

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43627 AN: 67656

Other (OTH) AF: 0.702 AC: 1460 AN: 2080

Alfa AF: 0.673 Hom.: 16982

Bravo AF: 0.744

Asia WGS AF: 0.821 AC: 2856 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.88
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs11623995; hg19: chr14-22905725;