rs10484890

chr6-10905813-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040274.3(SYCP2L):c.642-207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,128 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

SYCP2L (HGNC:21537): (synaptonemal complex protein 2 like) Predicted to be involved in meiotic nuclear division. Predicted to act upstream of or within negative regulation of cell death. Located in condensed chromosome, centromeric region and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYCP2L	NM_001040274.3	c.642-207C>T		intron_variant		ENST00000283141.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP2L	ENST00000283141.11	c.642-207C>T		intron_variant		1	NM_001040274.3	P1
SYCP2L	ENST00000341041.8	c.642-207C>T		intron_variant, NMD_transcript_variant		2
SYCP2L	ENST00000487561.2	c.302+2850C>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18522 AN: 152010 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.122 AC: 18528 AN: 152128 Hom.: 1307 Cov.: 32 AF XY: 0.121 AC XY: 9010 AN XY: 74362

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.106

Alfa AF: 0.132 Hom.: 1969

Bravo AF: 0.114

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.26
Dann	Benign	0.52

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: rs10484890; hg19: chr6-10906046;