Variant chr12-101733484-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001177949.2(SYCP3):c.453+91G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 1,166,508 control chromosomes in the GnomAD database, including 53,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7174 hom., cov: 32)

Exomes 𝑓: 0.30 ( 45990 hom. )

Consequence

SYCP3
NM_001177949.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.155

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 12-101733484-C-A is Benign according to our data. Variant chr12-101733484-C-A is described in ClinVar as [Benign]. Clinvar id is 1235117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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.453+91G>T		intron_variant		ENST00000392924.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP3	ENST00000392924.2 linkuse as main transcript	c.453+91G>T		intron_variant		1	NM_001177949.2	P1

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46455

AN:

151904

Hom.:

7175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.299

GnomAD4 exome

AF:

0.298

AC:

301820

AN:

1014486

Hom.:

45990

Cov.:

AF XY:

0.295

AC XY:

154709

AN XY:

523712

show subpopulations

Gnomad4 AFR exome

AF:

0.282

Gnomad4 AMR exome

AF:

0.336

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.373

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.382

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.306

AC:

46492

AN:

152022

Hom.:

7174

Cov.:

AF XY:

0.308

AC XY:

22875

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.308

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.393

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.294

Hom.:

10838

Bravo

AF:

0.298

Asia WGS

AF:

0.334

AC:

1158

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.8

DANN

Benign

0.50

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.

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