rs1225741

Variant names:

• chr6-10952010-G-A
• rs1225741
• NM_001040274.3:c.1955-3106G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-10952010-G-A
• chr6-10952010-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

SYCP2L Gene-Disease associations (from GenCC):

• premature ovarian failure 24

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia

LOC101928191 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040274.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYCP2L	NM_001040274.3	MANE Select	c.1955-3106G>A		intron	N/A	NP_001035364.2	Q5T4T6-1
	LOC101928191	NR_125851.1		n.417C>T		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYCP2L	ENST00000283141.11	TSL:1 MANE Select	c.1955-3106G>A		intron	N/A	ENSP00000283141.6	Q5T4T6-1
	SYCP2L	ENST00000341041.8	TSL:2	n.*1133-3106G>A		intron	N/A	ENSP00000340320.4	Q5T4T6-2

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

African (AFR) AF: 0.361 AC: 14964 AN: 41460

American (AMR) AF: 0.310 AC: 4733 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3468

East Asian (EAS) AF: 0.0890 AC: 461 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4824

European-Finnish (FIN) AF: 0.402 AC: 4234 AN: 10540

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30840 AN: 67982

Other (OTH) AF: 0.397 AC: 839 AN: 2114

Alfa AF: 0.429 Hom.: 39419

Bravo AF: 0.384

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.68
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1225741; hg19: chr6-10952243;