ENST00000448913.1:n.139C>T

Variant names:

• chr13-60274914-C-T
• rs9528094
• ENST00000448913.1:n.139C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448913.1(TARDBPP2):​n.139C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.531 in 1,411,864 control chromosomes in the GnomAD database, including 201,653 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 0.49 (18729 hom., cov: 32)
  • Exomes 𝑓: 0.54 (182924 hom.)
• Consequence: TARDBPP2 ENST00000448913.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15
• Publications: 7 publications found

Genes affected

TARDBPP2 (HGNC:39848): (TARDBP pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TARDBPP2		n.60274914C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TARDBPP2	ENST00000448913.1	n.139C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74586 AN: 151826 Hom.: 18711 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.536 AC: 675731 AN: 1259920 Hom.: 182924 Cov.: 22 AF XY: 0.536 AC XY: 339846 AN XY: 634050

African (AFR) AF: 0.378 AC: 11184 AN: 29588

American (AMR) AF: 0.475 AC: 20298 AN: 42718

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 9645 AN: 24416

East Asian (EAS) AF: 0.582 AC: 22257 AN: 38242

South Asian (SAS) AF: 0.550 AC: 44453 AN: 80876

European-Finnish (FIN) AF: 0.550 AC: 28376 AN: 51592

Middle Eastern (MID) AF: 0.383 AC: 2043 AN: 5330

European-Non Finnish (NFE) AF: 0.547 AC: 510707 AN: 934070

Other (OTH) AF: 0.504 AC: 26768 AN: 53088

GnomAD4 genome AF: 0.491 AC: 74654 AN: 151944 Hom.: 18729 Cov.: 32 AF XY: 0.493 AC XY: 36619 AN XY: 74254

African (AFR) AF: 0.396 AC: 16395 AN: 41442

American (AMR) AF: 0.459 AC: 7009 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2800 AN: 5142

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5839 AN: 10552

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37142 AN: 67942

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.522 Hom.: 86093

Bravo AF: 0.478

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.3
DANN	Benign	0.73
PhyloP100		5.2

Splicing

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

Other links and lift over

dbSNP: rs9528094; hg19: chr13-60849048;