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GeneBe

rs72561722

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153046.3(TDRD9):c.420+405G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 152,194 control chromosomes in the GnomAD database, including 79 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 0.023 ( 79 hom., cov: 33)

Consequence

TDRD9
NM_153046.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700
Variant links:
Genes affected
TDRD9 (HGNC:20122): (tudor domain containing 9) Predicted to enable RNA binding activity. Involved in spermatogenesis. Located in cytoplasm and nucleus. Implicated in spermatogenic failure 30. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0648 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TDRD9NM_153046.3 linkuse as main transcriptc.420+405G>A intron_variant ENST00000409874.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TDRD9ENST00000409874.9 linkuse as main transcriptc.420+405G>A intron_variant 5 NM_153046.3 P1Q8NDG6-1
TDRD9ENST00000496087.5 linkuse as main transcriptn.432+405G>A intron_variant, non_coding_transcript_variant 4
TDRD9ENST00000554571.1 linkuse as main transcriptn.295+405G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0230
AC:
3493
AN:
152076
Hom.:
79
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00420
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.0381
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.0708
Gnomad SAS
AF:
0.0396
Gnomad FIN
AF:
0.00888
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0271
Gnomad OTH
AF:
0.0330
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0229
AC:
3486
AN:
152194
Hom.:
79
Cov.:
33
AF XY:
0.0232
AC XY:
1729
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.00419
Gnomad4 AMR
AF:
0.0379
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.0707
Gnomad4 SAS
AF:
0.0399
Gnomad4 FIN
AF:
0.00888
Gnomad4 NFE
AF:
0.0270
Gnomad4 OTH
AF:
0.0327
Alfa
AF:
0.00831
Hom.:
6
Bravo
AF:
0.0245
Asia WGS
AF:
0.0330
AC:
116
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.0
Dann
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs75530420; hg19: chr14-104429918; API