Variant chr12-101729443-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.553-230G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 427,128 control chromosomes in the GnomAD database, including 76,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 30016 hom., cov: 32)

Exomes 𝑓: 0.57 ( 46696 hom. )

Consequence

SYCP3
NM_001177949.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.954

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=-0.96).

BP6

Variant 12-101729443-C-A is Benign according to our data. Variant chr12-101729443-C-A is described in ClinVar as [Benign]. Clinvar id is 1229163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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.553-230G>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.553-230G>T		intron_variant		1	NM_001177949.2	P1

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

93796

AN:

151834

Hom.:

29971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.762

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.893

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.607

GnomAD4 exome

AF:

0.572

AC:

157534

AN:

275178

Hom.:

46696

Cov.:

AF XY:

0.574

AC XY:

83833

AN XY:

146036

show subpopulations

Gnomad4 AFR exome

AF:

0.768

Gnomad4 AMR exome

AF:

0.571

Gnomad4 ASJ exome

AF:

0.570

Gnomad4 EAS exome

AF:

0.884

Gnomad4 SAS exome

AF:

0.618

Gnomad4 FIN exome

AF:

0.578

Gnomad4 NFE exome

AF:

0.525

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.618

AC:

93906

AN:

151950

Hom.:

30016

Cov.:

AF XY:

0.621

AC XY:

46140

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.762

Gnomad4 AMR

AF:

0.558

Gnomad4 ASJ

AF:

0.574

Gnomad4 EAS

AF:

0.892

Gnomad4 SAS

AF:

0.645

Gnomad4 FIN

AF:

0.600

Gnomad4 NFE

AF:

0.525

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.437

Hom.:

1179

Bravo

AF:

0.623

Asia WGS

AF:

0.794

AC:

2746

AN:

3466

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

DANN

Benign

0.23

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