3-44261632-A-G

Variant names:

• chr3-44261632-A-G
• rs9821268
• NM_001145030.2:c.2956-787A>G

Variant summary

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

The NM_001145030.2(TOPAZ1):​c.2956-787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,020 control chromosomes in the GnomAD database, including 18,236 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 0.48 (18236 hom., cov: 32)
• Consequence: TOPAZ1 NM_001145030.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 3 publications found

Genes affected

TOPAZ1 (HGNC:24746): (testis and ovary specific TOPAZ 1) Predicted to be involved in spermatid development and spermatocyte division. Predicted to act upstream of or within apoptotic process; ncRNA transcription; and positive regulation of meiotic cell cycle phase transition. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145030.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOPAZ1	NM_001145030.2	MANE Select	c.2956-787A>G		intron	N/A	NP_001138502.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOPAZ1	ENST00000309765.4	TSL:5 MANE Select	c.2956-787A>G		intron	N/A	ENSP00000310303.4

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72582 AN: 151902 Hom.: 18221 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.478 AC: 72639 AN: 152020 Hom.: 18236 Cov.: 32 AF XY: 0.487 AC XY: 36192 AN XY: 74302

African (AFR) AF: 0.366 AC: 15185 AN: 41488

American (AMR) AF: 0.544 AC: 8315 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4168 AN: 5172

South Asian (SAS) AF: 0.704 AC: 3384 AN: 4810

European-Finnish (FIN) AF: 0.540 AC: 5685 AN: 10536

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32458 AN: 67950

Other (OTH) AF: 0.471 AC: 992 AN: 2108

Alfa AF: 0.459 Hom.: 2147

Bravo AF: 0.473

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9821268; hg19: chr3-44303124;