Variant chr12-101731674-TATAAA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001177949.2(SYCP3):c.454-13_454-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,574,740 control chromosomes in the GnomAD database, including 3,282 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 328 hom., cov: 32)

Exomes 𝑓: 0.021 ( 2954 hom. )

Consequence

SYCP3
NM_001177949.2 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.48

Variant links:

Genes affected

SYCP3 (HGNC:18130): (synaptonemal complex protein 3) This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]

SYCP3 links:

CHPT1 (HGNC:17852): (choline phosphotransferase 1) Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

CHPT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-101731674-TATAAA-T is Benign according to our data. Variant chr12-101731674-TATAAA-T is described in ClinVar as [Benign]. Clinvar id is 306763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYCP3	NM_001177949.2 linkuse as main transcript	c.454-13_454-9del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000392924.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP3	ENST00000392924.2 linkuse as main transcript	c.454-13_454-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001177949.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0218

AC:

3318

AN:

152020

Hom.:

328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00183

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0103

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0205

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00466

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.0445

AC:

9705

AN:

217934

Hom.:

1076

AF XY:

0.0468

AC XY:

5551

AN XY:

118512

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00387

Gnomad ASJ exome

AF:

0.0293

Gnomad EAS exome

AF:

0.321

Gnomad SAS exome

AF:

0.123

Gnomad FIN exome

AF:

0.0204

Gnomad NFE exome

AF:

0.00446

Gnomad OTH exome

AF:

0.0272

GnomAD4 exome

AF:

0.0211

AC:

30064

AN:

1422602

Hom.:

2954

AF XY:

0.0239

AC XY:

16907

AN XY:

707214

show subpopulations

Gnomad4 AFR exome

AF:

0.00104

Gnomad4 AMR exome

AF:

0.00442

Gnomad4 ASJ exome

AF:

0.0303

Gnomad4 EAS exome

AF:

0.324

Gnomad4 SAS exome

AF:

0.123

Gnomad4 FIN exome

AF:

0.0186

Gnomad4 NFE exome

AF:

0.00339

Gnomad4 OTH exome

AF:

0.0332

GnomAD4 genome

AF:

0.0218

AC:

3321

AN:

152138

Hom.:

328

Cov.:

AF XY:

0.0264

AC XY:

1961

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.00183

Gnomad4 AMR

AF:

0.0104

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.312

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.0205

Gnomad4 NFE

AF:

0.00466

Gnomad4 OTH

AF:

0.0250

Alfa

AF:

0.0123

Hom.:

Bravo

AF:

0.0191

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Spermatogenic Failure

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over