rs1225741

chr6-10952010-G-Achr6-10952010-G-T

Variant summary

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

The NM_001040274.3(SYCP2L):c.1955-3106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,042 control chromosomes in the GnomAD database, including 12,098 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 0.39 (12098 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.984

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]

LOC101928191 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYCP2L	NM_001040274.3	c.1955-3106G>A		intron_variant		ENST00000283141.11
LOC101928191	NR_125851.1	n.417C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP2L	ENST00000283141.11	c.1955-3106G>A		intron_variant		1	NM_001040274.3	P1
SYCP2L	ENST00000341041.8	c.*1133-3106G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59182 AN: 151924 Hom.: 12098 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.389 AC: 59208 AN: 152042 Hom.: 12098 Cov.: 32 AF XY: 0.381 AC XY: 28306 AN XY: 74320

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.397

Alfa AF: 0.437 Hom.: 24315

Bravo AF: 0.384

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.6
Dann	Benign	0.68

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: rs1225741; hg19: chr6-10952243;