3-39132039-A-G

Position:

• chr3-39132039-A-G

Variant summary

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

The NM_001366900.1(TTC21A):​c.2562+944A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,868 control chromosomes in the GnomAD database, including 36,640 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 0.68 (36640 hom., cov: 31)
• Consequence: TTC21A NM_001366900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

TTC21A (HGNC:30761): (tetratricopeptide repeat domain 21A) Involved in flagellated sperm motility and spermatid development. Predicted to be located in cilium. Predicted to be part of intraciliary transport particle A. Implicated in spermatogenic failure 37. [provided by Alliance of Genome Resources, Apr 2022]

TTC21A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC21A	NM_001366900.1	c.2562+944A>G		intron_variant		ENST00000683103.1	NP_001353829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC21A	ENST00000683103.1	c.2562+944A>G		intron_variant			NM_001366900.1	ENSP00000507739.1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103751 AN: 151750 Hom.: 36637 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.684 AC: 103803 AN: 151868 Hom.: 36640 Cov.: 31 AF XY: 0.689 AC XY: 51119 AN XY: 74246

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.693

Alfa AF: 0.710 Hom.: 11414

Bravo AF: 0.667

Asia WGS AF: 0.734 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs784490; hg19: chr3-39173530;