19-32738959-AC-GT

Variant names:

• chr19-32738959-AC-GT
• NM_001366102.1:c.287_288delACinsGT
• TDRD12 p.Asp96Gly

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001366102.1(TDRD12):​c.287_288delACinsGT​(p.Asp96Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D96A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TDRD12 NM_001366102.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.04
• Publications: 0 publications found

Genes affected

TDRD12 (HGNC:25044): (tudor domain containing 12) Predicted to enable ATP binding activity; RNA helicase activity; and nucleic acid binding activity. Predicted to be involved in several processes, including gamete generation; gene silencing by RNA; and piRNA metabolic process. Predicted to be part of PET complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRD12	NM_001366102.1	MANE Select	c.287_288delACinsGT	p.Asp96Gly	missense	N/A	NP_001353031.1	A0A1W2PRK2
	TDRD12	NM_001437947.1		c.287_288delACinsGT	p.Asp96Gly	missense	N/A	NP_001424876.1	A0A2R8Y872
	TDRD12	NM_001438799.1		c.287_288delACinsGT	p.Asp96Gly	missense	N/A	NP_001425728.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRD12	ENST00000639142.2	TSL:5 MANE Select	c.287_288delACinsGT	p.Asp96Gly	missense	N/A	ENSP00000492643.2	A0A1W2PRK2
	TDRD12	ENST00000444215.6	TSL:1	c.287_288delACinsGT	p.Asp96Gly	missense	N/A	ENSP00000416248.2	Q587J7-1
	TDRD12	ENST00000647536.1		c.287_288delACinsGT	p.Asp96Gly	missense	N/A	ENSP00000496698.1	A0A2R8Y872

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-33229865;