2-238232864-A-G

Variant names:

• chr2-238232864-A-G
• rs11689432
• ENST00000799397.1:n.891A>G

Variant summary

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

The ENST00000799397.1(ENSG00000225057):​n.891A>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: ENSG00000225057 ENST00000799397.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83
• Publications: 9 publications found

Genes affected

ENSG00000225057 (HGNC:):

TARDBPP3 (HGNC:55122): (TARDBP pseudogene 3)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TARDBPP3	NR_026923.1	n.1179A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225057	ENST00000799397.1	n.891A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000225057	ENST00000799398.1	n.823A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000225057	ENST00000456601.1	n.906+275A>G		intron_variant	Intron 1 of 6	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

African (AFR) AF: 0.685 AC: 28423 AN: 41474

American (AMR) AF: 0.481 AC: 7345 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1747 AN: 5154

South Asian (SAS) AF: 0.524 AC: 2528 AN: 4824

European-Finnish (FIN) AF: 0.626 AC: 6608 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35707 AN: 67944

Other (OTH) AF: 0.563 AC: 1188 AN: 2112

Alfa AF: 0.565 Hom.: 10655

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
PhyloP100		2.8

Splicing

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

Other links and lift over

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