chr12-101731312-G-A

Position:

• chr12-101731312-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001177949.2(SYCP3):​c.552+256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,990 control chromosomes in the GnomAD database, including 2,774 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2774 hom., cov: 32)
• Consequence: SYCP3 NM_001177949.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.343

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]

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 12-101731312-G-A is Benign according to our data. Variant chr12-101731312-G-A is described in ClinVar as [Benign]. Clinvar id is 1270318.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYCP3	NM_001177949.2	c.552+256C>T		intron_variant		ENST00000392924.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP3	ENST00000392924.2	c.552+256C>T		intron_variant		1	NM_001177949.2	P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27034 AN: 151872 Hom.: 2766 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.178 AC: 27073 AN: 151990 Hom.: 2774 Cov.: 32 AF XY: 0.181 AC XY: 13415 AN XY: 74286

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.190

Alfa AF: 0.159 Hom.: 256

Bravo AF: 0.186

Asia WGS AF: 0.323 AC: 1105 AN: 3422

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

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
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.58

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: rs11110986; hg19: chr12-102125090;