rs722448

Variant names:

• chr14-22299752-C-T
• rs722448

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 0.632 in 150,782 control chromosomes in the GnomAD database, including 32,230 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 0.63 (32230 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22299752C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.271-98370G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95189 AN: 150664 Hom.: 32155 Cov.: 26

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.632 AC: 95324 AN: 150782 Hom.: 32230 Cov.: 26 AF XY: 0.635 AC XY: 46777 AN XY: 73624

African (AFR) AF: 0.883 AC: 36207 AN: 41020

American (AMR) AF: 0.609 AC: 9174 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4176 AN: 5168

South Asian (SAS) AF: 0.647 AC: 3079 AN: 4762

European-Finnish (FIN) AF: 0.509 AC: 5283 AN: 10370

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33784 AN: 67652

Other (OTH) AF: 0.608 AC: 1271 AN: 2090

Alfa AF: 0.534 Hom.: 37668

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs722448; hg19: chr14-22767645;