rs2733776

Variant names:

• chr14-22461795-A-G
• rs2733776

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 0.243 in 151,054 control chromosomes in the GnomAD database, including 4,671 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 0.24 (4671 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22461795A>G		intragenic_variant
TRD		n.22461795A>G		intragenic_variant
TRD-AS1	NR_148361.1	n.225+19446T>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+19446T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36621 AN: 150936 Hom.: 4668 Cov.: 26

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.243 AC: 36656 AN: 151054 Hom.: 4671 Cov.: 26 AF XY: 0.243 AC XY: 17949 AN XY: 73806

African (AFR) AF: 0.166 AC: 6825 AN: 41084

American (AMR) AF: 0.199 AC: 3013 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1086 AN: 3458

East Asian (EAS) AF: 0.175 AC: 903 AN: 5162

South Asian (SAS) AF: 0.334 AC: 1593 AN: 4776

European-Finnish (FIN) AF: 0.298 AC: 3105 AN: 10432

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19354 AN: 67734

Other (OTH) AF: 0.240 AC: 505 AN: 2100

Alfa AF: 0.279 Hom.: 3419

Bravo AF: 0.233

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.83
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs2733776; hg19: chr14-22930787;