rs11689432

Positions:

• chr2-238232864-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026923.1(TARDBPP3):​n.1179A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,010 control chromosomes in the GnomAD database, including 24,835 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 0.56 (24835 hom., cov: 32)
• Consequence: TARDBPP3 NR_026923.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83

Genes affected

TARDBPP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TARDBPP3	NR_026923.1	n.1179A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000456601.1	n.906+275A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85679 AN: 151892 Hom.: 24787 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.564 AC: 85791 AN: 152010 Hom.: 24835 Cov.: 32 AF XY: 0.566 AC XY: 42053 AN XY: 74272

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.563

Alfa AF: 0.537 Hom.: 7605

Bravo AF: 0.555

Asia WGS AF: 0.430 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11689432; hg19: chr2-239141505; COSMIC: COSV58538360;