rs2153157

chr6-10897255-G-A

Variant summary

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

The NM_001040274.3(SYCP2L):c.337-756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,980 control chromosomes in the GnomAD database, including 23,862 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 0.55 (23862 hom., cov: 32)
• Consequence: SYCP2L NM_001040274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYCP2L	NM_001040274.3	c.337-756G>A		intron_variant		ENST00000283141.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYCP2L	ENST00000283141.11	c.337-756G>A		intron_variant		1	NM_001040274.3	P1
SYCP2L	ENST00000341041.8	c.337-756G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82896 AN: 151862 Hom.: 23831 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.546 AC: 82969 AN: 151980 Hom.: 23862 Cov.: 32 AF XY: 0.542 AC XY: 40239 AN XY: 74268

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.539

Alfa AF: 0.498 Hom.: 44565

Bravo AF: 0.559

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.35
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: rs2153157; hg19: chr6-10897488; COSMIC: COSV51658250; COSMIC: COSV51658250;