rs1540268

Variant names:

• chr14-22307060-C-T
• rs1540268

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 0.692 in 146,524 control chromosomes in the GnomAD database, including 36,019 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 0.69 (36019 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22307060C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+93984G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.692 AC: 101341 AN: 146408 Hom.: 36015 Cov.: 25

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.692 AC: 101367 AN: 146524 Hom.: 36019 Cov.: 25 AF XY: 0.699 AC XY: 50076 AN XY: 71684

African (AFR) AF: 0.461 AC: 17170 AN: 37208

American (AMR) AF: 0.779 AC: 11582 AN: 14862

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2342 AN: 3410

East Asian (EAS) AF: 0.866 AC: 4465 AN: 5154

South Asian (SAS) AF: 0.782 AC: 3694 AN: 4722

European-Finnish (FIN) AF: 0.813 AC: 8441 AN: 10384

Middle Eastern (MID) AF: 0.668 AC: 191 AN: 286

European-Non Finnish (NFE) AF: 0.762 AC: 51478 AN: 67532

Other (OTH) AF: 0.707 AC: 1453 AN: 2056

Alfa AF: 0.732 Hom.: 182637

Bravo AF: 0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs1540268; hg19: chr14-22775479;